Contacts of the helix formed by residues 75 - 89 (chain L) in PDB entry 3D29
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
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Residue Dist Surf HB Arom Phob DC
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105D GLU* 4.4 5.1 + - - -
41L ILE* 4.5 0.2 - - - -
66L TYR* 5.4 0.6 + - - -
73L LYS* 3.6 11.1 + - - +
74L LEU* 1.3 78.1 - - - +
76L ILE* 1.3 61.3 + - - +
77L ASN* 2.6 25.9 + - - -
78L SER* 3.0 19.6 + - - -
79L ALA* 2.9 25.5 + - - +
104L LEU 5.8 0.2 - - - -
105L ASP 6.4 0.2 - - - -
106L GLU* 3.4 30.6 + - - -
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Residues in contact with ILE 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L ILE* 4.4 13.8 - - + +
74L LEU 3.7 1.0 + - - -
75L SER* 1.3 73.1 - - - +
77L ASN* 1.3 68.0 + - + +
79L ALA* 3.3 5.3 + - - +
80L ALA* 3.0 22.5 + - - +
101L ILE* 3.8 16.9 - - + +
102L ALA* 3.4 13.9 - - - +
103L GLY* 3.2 37.9 - - - +
104L LEU 3.8 23.3 + - - +
105L ASP* 4.2 14.6 - - + -
109L ALA* 3.8 12.3 - - + +
111L TYR* 3.8 24.9 - - + +
121L ARG* 6.0 0.2 - - - +
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Residues in contact with ASN 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ASP* 3.0 44.2 + - - +
105D GLU* 5.6 0.2 - - - +
75L SER* 2.6 30.0 + - - -
76L ILE* 1.3 83.6 - - + +
78L SER* 1.3 65.3 + - - +
80L ALA* 3.5 3.6 + - - +
81L ARG* 3.2 20.1 + - - +
106L GLU* 3.7 13.1 + - - +
111L TYR* 3.4 26.2 - - - +
119L TYR* 4.8 2.4 + - - -
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Residues in contact with SER 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D TYR 4.4 1.7 - - - +
103D TYR* 2.7 31.4 + - - +
105D GLU* 3.3 18.2 + - - +
74L LEU* 3.6 20.2 - - - -
75L SER* 3.0 25.5 + - - -
77L ASN* 1.3 84.9 + - - +
79L ALA* 1.3 64.9 + - - +
81L ARG* 3.2 4.3 + - - +
82L ASN* 3.0 21.8 + - - +
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Residues in contact with ALA 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L ILE* 3.8 15.7 - - + -
59L PHE* 3.5 28.0 - - + -
74L LEU* 3.9 12.9 - - + +
75L SER 2.9 12.1 + - - +
76L ILE* 3.3 9.4 + - - +
78L SER* 1.3 75.4 - - - +
80L ALA* 1.3 56.5 + - - +
82L ASN* 3.1 4.3 + - - +
83L ILE* 2.8 36.4 + - - +
101L ILE* 4.3 8.5 - - + -
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Residues in contact with ALA 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L ILE 3.0 12.8 + - - +
77L ASN 3.5 9.2 - - - +
78L SER 3.1 0.2 - - - -
79L ALA* 1.3 74.2 - - - +
81L ARG* 1.3 66.0 + - - +
83L ILE 3.3 0.7 + - - -
84L GLN* 3.1 20.1 + - - +
101L ILE* 4.3 2.4 - - + +
111L TYR* 3.6 33.7 - - + -
113L PHE* 3.4 25.6 - - + -
119L TYR* 3.9 12.8 - - + -
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Residues in contact with ARG 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ASN* 3.4 14.3 + - - -
101D LEU* 2.9 30.1 + - - +
102D TYR 3.0 20.9 - - - +
103D TYR 4.0 0.4 - - - -
104D ASP* 3.7 38.8 + - + +
57K THR* 4.0 25.6 + - - +
77L ASN 3.2 3.1 + - - +
78L SER 3.2 8.0 + - - +
80L ALA* 1.3 79.3 - - - +
82L ASN* 1.3 62.3 + - - +
84L GLN* 3.4 14.8 + - - +
85L HIS* 3.2 37.6 + - - -
119L TYR* 3.1 24.3 + - - +
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Residues in contact with ASN 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D TYR* 3.5 13.3 + - - +
103D TYR* 4.4 20.5 + - + -
59L PHE* 4.3 10.2 - - + -
62L SER* 2.5 35.9 + - - -
74L LEU* 5.4 3.4 - - + +
78L SER 3.0 13.0 + - - +
79L ALA* 3.1 12.3 + - - +
81L ARG* 1.3 77.9 - - - +
83L ILE* 1.3 62.4 + - - +
85L HIS* 3.1 11.0 + - - +
86L LEU* 3.0 27.7 + - - +
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Residues in contact with ILE 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L MET* 3.8 31.2 - - + -
55L LEU* 4.7 3.1 - - + -
59L PHE* 3.7 29.6 - - + -
79L ALA 2.8 19.8 + - - +
80L ALA 3.3 0.2 + - - -
82L ASN* 1.3 73.1 - - - +
84L GLN* 1.3 65.1 + - - +
86L LEU* 3.2 9.8 + - + +
87L LEU* 3.0 38.7 + - + +
99L THR* 4.5 1.6 - - - +
101L ILE* 3.8 27.4 - - + -
113L PHE* 3.8 30.3 - - + -
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Residues in contact with GLN 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K ALA* 5.7 1.2 + - - +
53K GLN* 3.4 26.8 + - - +
54K PHE* 4.0 28.7 - - + +
57K THR* 5.4 4.7 + - - +
80L ALA 3.1 12.5 + - - +
81L ARG* 3.5 25.6 + - - +
82L ASN 3.1 0.2 - - - -
83L ILE* 1.3 76.3 - - - +
85L HIS* 1.3 62.5 + - - +
87L LEU* 3.9 0.9 - - - +
88L TYR* 2.8 29.6 + - + +
113L PHE* 4.2 2.4 - - - -
117L GLY* 3.2 35.8 + - - +
118L SER* 4.6 0.2 - - - +
119L TYR* 3.3 24.8 - - + -
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Residues in contact with HIS 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 3.2 37.9 - - + +
102D TYR* 3.1 42.3 - + + -
54K PHE* 3.7 31.7 - + - -
57K THR* 6.1 0.2 - - + -
81L ARG* 3.2 26.3 + - - -
82L ASN* 3.1 15.7 + - - +
84L GLN* 1.3 83.6 + - - +
86L LEU* 1.3 65.1 + - - +
88L TYR* 4.8 3.4 - - - -
89L GLY* 2.9 22.5 + - - -
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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
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55L LEU* 4.1 17.7 - - + -
58L ARG* 3.6 56.1 + - + +
59L PHE* 3.8 40.6 - - + +
62L SER* 5.3 2.2 - - - -
82L ASN* 3.0 23.3 + - - +
83L ILE* 3.2 20.2 + - + +
85L HIS* 1.3 78.0 - - - +
87L LEU* 1.3 62.2 + - - +
89L GLY* 3.5 7.6 + - - -
90L LYS 3.9 1.9 + - - -
95L TYR* 3.8 9.1 - - - -
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Residues in contact with LEU 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L LEU* 3.7 26.0 - - + -
83L ILE* 3.0 28.7 + - + +
84L GLN 3.9 1.3 - - - +
86L LEU* 1.3 73.2 - - - +
88L TYR* 1.3 63.0 + - - +
89L GLY 3.0 4.7 - - - -
90L LYS* 3.0 22.2 + - - +
91L ARG* 4.4 0.9 - - - -
94L PRO* 5.5 1.0 - - - +
95L TYR* 3.8 23.4 + - + -
97L VAL* 4.3 6.5 - - + -
99L THR* 4.2 4.9 - - + -
113L PHE* 3.8 20.4 - - + -
114L ASP 3.5 20.2 - - - +
115L PRO 3.6 18.4 - - - +
116L VAL* 4.2 6.0 - - - +
117L GLY* 3.7 18.4 - - - +
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Residues in contact with TYR 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K ALA* 3.8 20.2 - - + -
51K ASP* 2.6 29.4 + - - -
54K PHE* 3.5 55.4 - + + -
55K TRP* 3.0 29.4 + + - -
95K LEU* 3.3 9.0 - - - +
84L GLN* 2.8 22.8 + - + +
85L HIS 4.5 0.4 - - - +
87L LEU* 1.3 71.1 - - - +
89L GLY* 1.3 65.9 + - - +
90L LYS 3.0 0.2 - - - -
91L ARG* 3.0 38.2 + - + +
92L PHE* 5.8 2.2 - + - -
116L VAL 3.2 23.7 + - - +
117L GLY* 5.4 0.4 - - - -
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Residues in contact with GLY 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L ARG* 5.9 1.6 - - - -
85L HIS 2.9 19.8 + - - -
86L LEU 3.9 3.6 - - - -
87L LEU 3.0 1.0 - - - -
88L TYR* 1.3 79.5 - - - +
90L LYS* 1.3 61.5 + - - +
91L ARG 3.3 1.5 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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