Contacts of the helix formed by residues 75 - 95 (chain L) in PDB entry 4GGF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 75 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASP* 5.3 0.2 - - - +
19L PHE* 3.7 2.0 - - - -
30L ASP 4.5 1.1 - - - -
31L THR* 4.0 16.9 - - - +
73L GLN 4.0 0.6 + - - -
74L LEU* 1.3 75.9 - - - +
76L PHE* 1.3 64.7 + - - +
77L GLU* 3.6 16.1 + - - +
78L GLU* 3.1 36.0 + - - +
79L PHE* 2.9 21.7 + - - +
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Residues in contact with PHE 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K GLY* 3.4 29.4 - - - -
80K VAL* 4.1 7.6 - - + -
83K HIS* 3.4 46.3 - + + +
12L ILE* 5.9 0.2 - - + -
15L ILE* 3.9 26.2 - - + -
16L ILE* 3.6 31.4 - - + -
19L PHE* 3.4 38.6 - + + -
30L ASP 4.6 1.8 + - - -
75L SER* 1.3 74.7 - - - +
77L GLU* 1.3 62.3 + - - +
79L PHE* 3.2 5.0 + + - +
80L ILE* 2.8 48.3 + - + +
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Residues in contact with GLU 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 2.8 45.4 + - - +
62A THR* 3.7 13.9 + - - +
63A ASP* 4.1 7.6 - - + -
80K VAL* 4.0 25.0 - - + +
83K HIS* 4.7 11.8 + - - -
84K LYS* 5.9 2.3 - - - +
75L SER* 3.7 18.0 - - - +
76L PHE* 1.3 83.5 + - - +
78L GLU* 1.3 64.2 + - - +
80L ILE* 3.3 19.1 - - - +
81L MET* 4.0 0.3 - - - +
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Residues in contact with GLU 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 4.1 5.4 - - - +
63A ASP* 4.2 7.9 - - + +
66L LEU* 3.3 28.6 - - - +
67L ASP* 3.7 0.6 - - - +
68L THR* 3.2 34.6 + - - +
69L ASN* 3.0 17.3 + - - +
73L GLN 2.9 10.9 - - - +
74L LEU* 3.2 5.8 - - + +
75L SER* 3.1 26.9 + - - +
77L GLU* 1.3 80.6 - - - +
79L PHE* 1.3 61.6 + - - +
81L MET* 3.4 17.2 + - - +
204L CA 2.3 31.2 - - - -
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Residues in contact with PHE 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K LEU* 5.0 3.1 - - + -
15L ILE* 4.2 12.1 - - + -
18L THR* 5.9 0.2 - - + -
19L PHE* 3.7 31.4 - + + -
32L LEU* 3.9 13.0 - - + -
37L PHE* 4.4 20.0 - + - -
40L LEU* 3.8 37.9 - - + -
66L LEU* 5.1 0.7 - - - -
74L LEU* 4.5 11.8 - - + +
75L SER 2.9 16.2 + - - +
76L PHE* 3.6 10.5 - + - +
78L GLU* 1.3 77.6 - - - +
80L ILE* 1.3 59.0 + - - +
82L LEU* 2.9 31.0 + - + +
83L MET* 3.5 46.0 + - + -
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Residues in contact with ILE 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 4.3 2.0 - - + -
75K VAL* 4.3 7.0 - - + +
76K ILE* 3.9 34.9 - - + +
79K GLY* 3.7 30.5 - - - -
80K VAL* 4.1 15.9 - - + -
12L ILE* 6.0 1.1 - - + -
15L ILE* 4.9 8.1 - - + -
76L PHE* 2.8 36.6 + - + +
77L GLU 3.3 17.9 - - - +
79L PHE* 1.3 73.4 - - - +
81L MET* 1.3 63.5 + - - +
83L MET* 3.1 19.3 + - + -
84L ALA* 3.0 22.2 + - - +
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Residues in contact with MET 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 5.0 1.6 - - + -
61A ASN* 3.2 41.7 - - + +
63A ASP* 5.1 0.7 - - - +
67A ASN* 3.3 26.9 - - - +
69A GLN* 4.3 7.6 - - + +
70A GLU* 3.7 26.7 - - + +
76K ILE* 3.8 28.0 - - + -
66L LEU* 4.1 9.2 - - + -
68L THR* 6.4 1.1 - - + -
78L GLU* 3.7 10.1 - - - +
79L PHE 3.1 1.0 + - - -
80L ILE* 1.3 78.3 - - - +
82L LEU* 1.3 62.4 + - - +
84L ALA* 3.9 4.0 - - - +
85L ARG* 3.0 44.6 + - - +
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Residues in contact with LEU 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L PHE* 3.9 32.1 - - + -
45L LEU* 4.1 15.3 - - + -
49L LEU* 4.8 8.3 - - + -
62L ILE* 4.2 19.5 - - + -
66L LEU* 3.8 19.3 - - + +
79L PHE* 2.9 16.9 + - + +
81L MET* 1.3 80.1 - - - +
83L MET* 1.3 71.4 + - + +
85L ARG* 3.3 10.8 + - + +
86L LEU* 2.9 49.8 + - + +
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Residues in contact with MET 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K LEU* 3.9 27.4 - - + -
9K LEU* 4.1 22.6 - - + +
15L ILE* 3.8 18.8 - - + -
45L LEU* 4.1 14.6 - - + -
79L PHE* 3.5 46.9 - - + +
80L ILE* 3.1 16.5 + - + +
82L LEU* 1.3 98.0 - - + +
84L ALA* 1.3 61.0 + - - +
86L LEU* 3.4 6.7 + - + +
87L THR* 2.8 31.6 + - - -
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Residues in contact with ALA 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 6.1 0.4 - - - +
72K LEU* 3.8 20.8 - - + +
75K VAL* 6.3 2.0 - - + -
76K ILE* 3.8 31.4 - - + -
80L ILE* 3.0 14.7 + - + +
81L MET* 3.9 5.2 - - - +
83L MET* 1.3 76.6 - - - +
85L ARG* 1.3 58.3 + - + +
87L THR* 3.3 6.6 + - - -
88L TRP* 2.9 30.8 + - - +
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Residues in contact with ARG 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN* 3.6 14.5 - - - +
69A GLN* 2.9 39.5 + - - +
88C TRP* 4.8 10.8 - - + -
205C GOL 2.5 35.3 + - - -
62L ILE* 6.0 1.8 - - - +
65L ASP* 3.0 17.4 + - - -
66L LEU* 3.7 24.3 - - - +
81L MET* 3.0 27.7 + - - +
82L LEU* 3.6 14.3 - - + +
84L ALA* 1.3 77.3 - - + +
86L LEU* 1.3 60.0 + - + +
88L TRP* 3.4 10.6 - - - +
89L ALA* 2.8 28.6 + - - +
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Residues in contact with LEU 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K LEU* 3.9 16.6 - - + -
45L LEU* 3.7 38.6 - - + -
48L PHE* 4.1 13.4 - - + -
49L LEU* 4.1 26.7 - - + -
82L LEU* 2.9 38.5 + - + +
83L MET* 3.9 4.3 - - + +
85L ARG* 1.3 76.7 - - + +
87L THR* 1.3 56.6 + - - +
89L ALA* 3.6 6.5 - - + +
90L SER* 2.8 34.7 + - - -
109L LEU* 4.2 16.1 - - + +
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Residues in contact with THR 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K LEU* 3.5 44.5 - - - +
12K ILE* 4.1 12.5 - - + +
13K ILE* 3.5 10.3 - - + +
68K PHE* 3.7 24.9 - - + -
72K LEU* 4.1 13.0 - - + -
83L MET 2.8 22.6 + - - -
84L ALA* 3.6 4.5 - - - -
86L LEU* 1.3 75.6 - - - +
88L TRP* 1.3 63.7 + - - +
90L SER* 3.3 3.6 + - - -
91L HIS* 3.0 21.1 + - - +
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Residues in contact with TRP 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ARG* 4.6 20.9 - - + -
88C TRP* 4.4 27.4 - + - +
68K PHE* 3.7 29.6 - + + -
69K GLN* 3.3 55.9 - - + -
72K LEU* 4.0 9.8 - - + +
84L ALA 2.9 18.0 + - - +
85L ARG* 3.4 9.4 - - - +
87L THR* 1.3 75.9 - - - +
89L ALA* 1.3 60.6 + - + +
91L HIS* 3.2 6.9 + - - +
92L GLU* 2.9 69.6 + - + +
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Residues in contact with ALA 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85L ARG 2.8 22.1 + - - +
86L LEU* 3.3 13.0 + - + +
88L TRP* 1.3 76.8 - - + +
90L SER* 1.3 62.8 + - - +
92L GLU* 3.4 8.8 + - - +
93L LYS* 3.0 22.7 + - - +
109L LEU* 4.1 19.2 - - + +
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Residues in contact with SER 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K LEU 6.2 0.2 - - - -
10K ASN* 2.8 28.0 + - - -
13K ILE* 3.9 3.1 - - - -
48L PHE* 3.9 5.9 - - - -
86L LEU 2.8 20.7 + - - -
87L THR* 3.7 4.9 - - - -
88L TRP 3.2 0.4 - - - -
89L ALA* 1.3 73.1 - - - +
91L HIS* 1.3 59.2 + - - +
93L LYS* 3.2 4.5 + - - +
94L MET* 2.9 30.8 + - - +
108L GLY* 3.5 4.5 - - - -
109L LEU* 3.0 35.9 + - - +
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Residues in contact with HIS 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13K ILE* 3.6 18.5 - - + +
17K HIS* 3.1 14.2 - + - -
27K HIS* 3.3 23.3 - + - -
68K PHE* 3.8 33.4 - + + +
87L THR 3.0 13.2 + - - +
88L TRP* 3.6 8.7 - - - +
90L SER* 1.3 78.0 - - - +
92L GLU* 1.3 68.2 + - - +
94L MET* 3.2 14.8 + - - +
95L HIS* 3.2 22.3 + + - -
105L HIS* 3.3 13.9 - + - -
202L MN 2.2 35.5 + - - -
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Residues in contact with GLU 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ARG* 6.1 0.2 - - - -
88L TRP* 2.9 66.9 + - + +
89L ALA* 3.6 7.6 - - - +
91L HIS* 1.3 82.8 + - - +
93L LYS* 1.3 56.3 + - - +
95L HIS* 2.9 24.6 + - - +
96L GLU* 3.0 13.7 + - - +
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Residues in contact with LYS 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L ALA 3.0 13.6 + - - +
90L SER 3.2 8.7 + - - +
92L GLU* 1.3 74.2 - - - +
94L MET* 1.3 63.0 + - - +
95L HIS 3.1 0.9 + - - -
96L GLU* 3.1 41.9 + - - +
106L LYS* 4.4 5.9 - - - +
107L PRO* 3.6 17.5 + - - +
108L GLY 3.2 26.8 + - - -
109L LEU* 4.1 16.1 - - + +
110L GLY 5.2 0.8 - - - +
111L GLU* 3.7 16.0 + - - +
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Residues in contact with MET 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K ASN* 3.5 33.2 - - + +
13K ILE* 3.6 20.9 - - + -
14K ASP* 5.9 2.2 - - - +
90L SER* 2.9 20.3 + - - +
91L HIS* 3.2 15.2 + - - +
93L LYS* 1.3 75.2 - - - +
95L HIS* 1.3 58.4 + - - +
96L GLU 3.5 0.2 - - - -
98L ASP* 5.6 0.3 - - - +
104L HIS 4.0 3.3 - - - +
105L HIS* 3.6 45.4 - - + -
106L LYS* 2.8 53.1 + - - +
107L PRO 3.8 1.6 - - - -
108L GLY* 3.7 11.7 - - - +
112L GLY 5.6 0.7 - - - +
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Residues in contact with HIS 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C HIS* 4.3 11.1 + + - +
26K PHE* 5.4 0.2 - + - -
27K HIS* 3.2 12.1 + + - -
91L HIS* 3.2 38.7 + + - +
92L GLU* 2.9 13.1 + - - +
94L MET* 1.3 75.9 - - - +
96L GLU* 1.3 65.2 + - - +
97L GLY 3.3 1.0 + - - -
98L ASP* 2.8 45.9 + - + +
103L HIS* 3.5 14.6 - + - -
104L HIS 3.3 22.0 + - - -
105L HIS* 3.2 5.7 - + - -
106L LYS* 5.2 0.7 - - - -
202L MN 2.3 29.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il