Contacts of the helix formed by residues 67 - 86 (chain U) 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 ASN 67 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68T THR* 6.0 6.1 - - + +
81T MET* 3.5 22.4 - - - +
85T ARG* 3.6 12.3 - - - +
16U TYR* 3.2 11.2 - - - -
27U HIS* 3.4 16.8 - - + +
61U ASN* 5.5 0.6 + - - +
63U ASP* 5.7 1.8 + - - +
65U ALA* 3.9 1.7 - - + -
66U VAL* 1.3 73.7 - - - +
68U PHE* 1.3 60.4 + - - +
69U GLN* 3.1 33.5 + - - +
70U GLU* 2.8 37.5 + - - +
71U PHE* 3.0 26.0 + - - +
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Residues in contact with PHE 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U ILE* 4.8 0.2 - - + -
13U ILE* 3.9 20.6 - - + -
16U TYR* 3.5 44.1 + + + -
17U HIS* 4.9 1.3 - + - -
27U HIS* 4.5 5.9 + - + +
67U ASN* 1.3 76.3 - - - +
69U GLN* 1.3 63.0 + - - +
71U PHE* 3.2 24.9 + + - +
72U LEU* 2.9 47.2 + - + +
87V THR* 3.7 29.2 - - + -
88V TRP* 3.9 17.3 - + + -
91V HIS* 3.6 44.4 - - + +
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Residues in contact with GLN 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81T MET* 4.3 14.1 + - + +
84T ALA* 6.2 0.6 - - - +
85T ARG* 2.8 45.1 + - - +
67U ASN* 3.1 29.1 + - - +
68U PHE* 1.3 80.1 + - - +
70U GLU* 1.3 65.5 + - + +
72U LEU* 3.2 21.0 + - + +
73U ILE* 3.6 9.2 + - - +
88V TRP* 3.2 38.5 - - + -
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Residues in contact with GLU 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81T MET* 3.6 12.1 - - + +
58U LEU* 3.0 32.6 - - - +
59U ASP* 4.1 0.4 - - - -
60U ILE* 2.9 30.7 + - + +
61U ASN* 3.0 9.6 + - - +
65U ALA 3.0 3.9 - - - +
66U VAL* 3.3 9.5 - - + -
67U ASN* 2.8 43.5 + - - +
69U GLN* 1.3 75.6 - - + +
71U PHE* 1.3 63.6 + - - +
73U ILE* 3.1 28.9 + - - +
101U CA 2.4 30.6 - - - -
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Residues in contact with PHE 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U ILE* 3.8 20.0 - - + -
15U VAL* 4.6 2.7 - - + -
16U TYR* 3.6 38.8 - + + -
34U LEU* 5.8 1.3 - - + -
37U LEU* 3.9 33.7 - - + -
58U LEU* 5.3 1.3 - - + -
66U VAL* 3.5 10.4 - - + +
67U ASN 3.0 15.5 + - - +
68U PHE* 3.3 26.2 - + - +
70U GLU* 1.3 74.3 - - - +
72U LEU* 1.3 64.4 + - + +
74U LEU* 3.1 30.9 + - + +
75U VAL* 3.1 36.7 + - + +
8V LEU* 4.3 16.8 - - + -
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Residues in contact with LEU 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U ILE* 4.5 2.9 - - + -
68U PHE* 2.9 52.5 + - + +
69U GLN* 3.5 11.2 - - + +
70U GLU 3.2 1.0 - - - -
71U PHE* 1.3 76.2 - - - +
73U ILE* 1.3 55.2 + - - +
75U VAL* 3.7 22.2 - - + +
76U ILE* 2.9 36.5 + - + +
84V ALA* 3.7 35.2 - - + +
87V THR* 4.1 15.0 - - + -
88V TRP* 3.9 18.8 - - + +
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Residues in contact with ILE 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S ILE* 3.7 39.7 - - + +
73S ILE* 4.4 13.5 - - + -
54U TRP* 5.4 0.2 - - + -
57U GLU* 5.0 1.8 - - + +
58U LEU* 3.6 18.4 - - + +
60U ILE* 3.7 35.7 - - + -
69U GLN 3.6 6.2 + - - +
70U GLU* 3.1 22.3 + - - +
72U LEU* 1.3 76.4 - - - +
74U LEU* 1.3 57.1 + - - +
76U ILE* 3.4 5.0 + - + +
77U LYS* 3.0 39.1 + - + +
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Residues in contact with LEU 74 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34U LEU* 4.7 4.0 - - + -
37U LEU* 4.0 20.9 - - + -
38U LEU* 3.9 22.9 - - + -
46U ILE* 4.2 0.9 - - + -
54U TRP* 3.7 40.8 - - + -
58U LEU* 3.8 25.5 - - + +
71U PHE* 3.1 23.8 + - + +
73U ILE* 1.3 76.8 - - - +
75U VAL* 1.3 59.5 + - - +
77U LYS* 3.8 3.1 - - - -
78U MET* 2.8 58.7 + - + +
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Residues in contact with VAL 75 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U ILE* 4.0 31.9 - - + -
71U PHE* 3.1 49.2 + - + +
72U LEU* 3.3 16.5 + - + +
74U LEU* 1.3 74.5 - - - +
76U ILE* 1.3 60.7 + - + +
78U MET* 3.4 7.3 + - - +
79U GLY* 2.9 27.2 + - - -
8V LEU* 4.4 7.9 - - + -
12V ILE* 4.3 12.8 - - + +
15V ILE* 5.7 2.9 - - + -
80V ILE* 4.2 6.1 - - + +
84V ALA* 6.3 2.2 - - + -
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Residues in contact with ILE 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S ILE* 3.8 23.3 - - + +
61S ASN* 3.8 31.2 - - + -
72U LEU* 2.9 25.5 + - + +
73U ILE* 3.6 4.5 - - + +
75U VAL* 1.3 77.2 - - + +
77U LYS* 1.3 57.1 + - - +
79U GLY* 3.3 1.9 + - - -
80U VAL* 3.0 30.0 + - + +
80V ILE* 3.7 23.7 - - + +
81V MET* 4.1 19.7 - - + -
84V ALA* 3.6 31.2 - - + -
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Residues in contact with LYS 77 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S LYS 5.5 4.2 + - - -
57S GLU* 5.2 2.6 + - - +
59S ASP 5.3 0.9 - - - -
60S ILE* 3.6 51.7 - - + +
62S THR* 6.0 2.5 - - - -
46U ILE* 4.8 3.3 - - + +
49U LYS* 4.9 3.1 - - - +
54U TRP* 4.1 29.6 - - + -
57U GLU* 4.2 16.2 + - - -
73U ILE* 3.0 25.0 + - + +
74U LEU 3.3 2.9 + - - +
76U ILE* 1.3 75.3 - - - +
78U MET* 1.3 58.4 + - - +
80U VAL* 3.5 6.0 + - - +
81U ALA* 2.9 30.8 + - - +
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Residues in contact with MET 78 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37U LEU* 6.1 0.2 - - - -
41U GLU 3.9 6.3 - - - +
42U SER* 3.9 14.6 - - - -
43U PRO* 3.9 26.5 - - + -
45U TYR* 4.6 1.4 + - - -
46U ILE* 3.9 25.1 - - + -
74U LEU* 2.8 43.4 + - + +
75U VAL* 3.7 1.3 - - - +
77U LYS* 1.3 77.1 - - - +
79U GLY* 1.3 57.0 + - - +
81U ALA* 3.8 1.2 - - - +
82U ALA* 2.9 31.7 + - - +
8V LEU* 3.7 34.3 - - + -
9V GLU* 4.8 4.9 - - + -
12V ILE* 3.6 20.6 - - + -
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Residues in contact with GLY 79 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75U VAL 2.9 11.6 + - - -
76U ILE 3.3 0.2 + - - -
78U MET* 1.3 72.5 - - - +
80U VAL* 1.3 59.6 + - - +
82U ALA* 3.9 1.0 - - - +
83U HIS 2.9 24.8 + - - -
12V ILE* 3.8 22.1 - - - +
16V ILE* 4.2 1.0 - - - +
76V PHE* 3.2 18.2 - - - -
80V ILE* 3.6 17.5 - - - -
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Residues in contact with VAL 80 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60S ILE 5.4 0.9 - - - +
61S ASN* 4.0 21.8 - - - +
62S THR* 3.8 19.1 - - - +
76U ILE 3.0 21.2 + - - +
77U LYS* 3.9 6.7 - - - +
79U GLY* 1.3 75.6 - - - +
81U ALA* 1.3 58.9 + - - +
83U HIS* 3.4 3.5 + - - +
84U LYS* 3.0 32.4 + - + +
76V PHE* 4.0 7.4 - - + -
77V GLU* 3.8 26.2 - - + +
80V ILE* 4.1 20.0 - - + -
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Residues in contact with ALA 81 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U TYR* 3.8 24.7 - - + -
46U ILE* 4.3 9.0 - - + -
77U LYS 2.9 19.5 + - - +
78U MET 3.8 3.6 - - - +
80U VAL* 1.3 78.9 - - - +
82U ALA* 1.3 61.6 + - - +
84U LYS* 3.3 8.3 + - - +
85U LYS* 3.1 28.4 + - - +
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Residues in contact with ALA 82 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U TYR* 3.5 18.3 + - - +
78U MET 2.9 19.3 + - - +
79U GLY 3.9 1.1 - - - +
81U ALA* 1.3 73.9 - - - +
83U HIS* 1.3 64.9 + - - +
85U LYS* 3.4 6.0 + - - +
86U SER* 3.3 23.2 + - - -
12V ILE* 3.9 12.6 - - + -
13V GLU* 4.3 9.0 - - - +
16V ILE* 3.7 17.7 - - + +
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Residues in contact with HIS 83 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79U GLY 2.9 9.3 + - - +
80U VAL 3.8 3.0 + - - +
82U ALA* 1.3 75.6 - - - +
84U LYS* 1.3 67.2 + - - +
86U SER* 3.3 22.1 - - - -
87U HIS* 3.7 4.0 + - + +
16V ILE* 3.5 22.4 - - + +
19V PHE* 4.2 4.6 - + - -
30V ASP* 2.8 42.6 + - - -
76V PHE* 3.4 60.6 - + + +
77V GLU* 4.8 11.9 + - - -
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Residues in contact with LYS 84 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80U VAL* 3.0 22.8 + - + +
81U ALA* 3.6 8.3 - - - +
82U ALA 3.3 0.2 - - - -
83U HIS* 1.3 82.6 + - - +
85U LYS* 1.3 60.5 - - - +
87U HIS* 3.1 32.7 + - + +
77V GLU* 5.6 6.3 - - - +
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Residues in contact with LYS 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45U TYR* 3.7 55.7 - - + +
81U ALA* 3.1 19.8 + - - +
82U ALA* 3.6 7.9 - - - +
83U HIS 3.3 0.2 - - - -
84U LYS* 1.3 70.8 - - - +
86U SER* 1.3 55.3 + - - +
87U HIS 2.8 28.2 + - - +
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Residues in contact with SER 86 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82U ALA 3.3 11.1 + - - -
83U HIS* 3.3 18.6 - - - -
85U LYS* 1.3 75.8 - - - +
87U HIS* 1.3 56.3 + - - +
13V GLU* 5.3 5.7 + - - -
16V ILE* 4.5 15.7 - - - +
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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