Contacts of the helix formed by residues 67 - 87 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S TYR* 3.2 11.9 - - - -
27S HIS* 3.3 16.4 - - + +
63S ASP* 5.7 1.8 + - - -
65S ALA* 3.9 1.0 + - - +
66S VAL* 1.3 74.0 - - - +
68S PHE* 1.3 63.9 + - - +
69S GLN* 3.2 28.5 + - - +
70S GLU* 2.8 41.3 + - - +
71S PHE* 2.9 20.1 + - - +
205T GOL 5.3 0.4 - - - +
68V THR* 5.5 9.3 - - + +
81V MET* 3.2 35.2 - - - +
85V ARG* 3.7 6.7 - - - +
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Residues in contact with PHE 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S ILE* 3.7 19.1 - - + -
16S TYR* 3.5 43.8 + + + -
17S HIS* 5.0 0.9 - + - -
27S HIS* 4.4 2.0 + - + +
67S ASN* 1.3 77.0 - - - +
69S GLN* 1.3 65.1 + - - +
71S PHE* 3.2 26.0 + + - +
72S LEU* 3.0 35.8 + - + +
87T THR* 3.7 33.7 - - + -
88T TRP* 3.8 16.2 - + - -
91T HIS* 3.6 35.4 - - + +
205T GOL 3.7 18.5 + - - +
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Residues in contact with GLN 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67S ASN* 3.2 16.5 + - - +
68S PHE* 1.3 76.7 - - - +
70S GLU* 1.3 62.3 + - + +
72S LEU* 3.2 20.2 + - + +
73S ILE* 3.6 9.5 + - - +
88T TRP* 2.9 37.8 - - + -
205T GOL 2.9 23.7 + - - -
81V MET* 3.2 33.3 - - - -
85V ARG* 3.2 25.0 + - + +
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Residues in contact with GLU 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58S LEU* 3.2 31.0 - - - +
60S ILE* 2.9 27.6 + - + +
61S ASN* 3.1 9.0 + - - +
65S ALA 3.0 3.9 - - - +
66S VAL* 3.3 9.9 - - + -
67S ASN* 2.8 47.0 + - - +
69S GLN* 1.3 76.1 - - + +
71S PHE* 1.3 64.6 + - - +
73S ILE* 3.1 28.9 + - + +
101S CA 2.5 31.3 - - - -
81V MET* 3.6 9.5 - - + +
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Residues in contact with PHE 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S ILE* 3.7 22.2 - - + -
15S VAL* 4.6 2.9 - - + -
16S TYR* 3.5 46.0 - + + -
34S LEU* 5.8 1.3 - - + -
37S LEU* 3.9 28.7 - - + -
58S LEU* 5.4 0.9 - - + -
66S VAL* 3.5 11.7 - - + +
67S ASN 2.9 14.5 + - - +
68S PHE* 3.4 21.3 - + - +
70S GLU* 1.3 75.8 - - - +
72S LEU* 1.3 60.0 + - + +
74S LEU* 2.9 39.7 + - + +
75S VAL* 3.0 35.9 + - + +
8T LEU* 4.4 14.8 - - + -
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Residues in contact with LEU 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S ILE* 4.5 2.9 - - + -
68S PHE* 3.0 45.9 + - + +
69S GLN* 3.5 11.2 - - - +
70S GLU 3.2 0.4 - - - -
71S PHE* 1.3 76.4 - - + +
73S ILE* 1.3 56.9 + - - +
75S VAL* 3.6 21.8 - - + +
76S ILE* 2.9 37.5 + - + +
84T ALA* 3.6 35.7 - - + +
87T THR* 4.0 15.5 - - + -
88T TRP* 4.0 23.8 - - + +
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Residues in contact with ILE 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54S TRP* 5.6 0.2 - - + -
57S GLU* 5.0 2.0 - - + +
58S LEU* 3.8 17.0 - - + +
60S ILE* 3.9 32.1 - - + -
69S GLN 3.6 7.4 + - - +
70S GLU* 3.1 21.4 + - + +
72S LEU* 1.3 77.1 - - - +
74S LEU* 1.3 61.0 + - - +
76S ILE* 3.3 4.7 + - + +
77S LYS* 3.0 36.5 + - + +
60U ILE* 3.7 37.5 - - + -
73U ILE* 4.4 14.8 - - + -
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Residues in contact with LEU 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S LEU* 5.0 2.7 - - + -
37S LEU* 3.9 27.4 - - + -
38S LEU* 4.1 11.9 - - + -
46S ILE* 4.2 5.4 - - + -
54S TRP* 3.7 41.1 - - + -
58S LEU* 3.7 26.0 - - + +
71S PHE* 2.9 23.9 + - + +
73S ILE* 1.3 76.9 - - - +
75S VAL* 1.3 60.8 + - - +
77S LYS* 3.2 1.3 + - - -
78S MET* 2.8 59.3 + - + +
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Residues in contact with VAL 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S ILE* 3.9 31.9 - - + -
71S PHE* 3.0 47.7 + - + +
72S LEU* 3.6 16.4 - - + +
73S ILE 3.3 0.2 - - - -
74S LEU* 1.3 75.8 - - - +
76S ILE* 1.3 62.3 + - + +
78S MET* 3.3 6.3 + - - +
79S GLY* 2.8 27.9 + - - -
8T LEU* 4.4 7.9 - - + -
12T ILE* 4.4 13.3 - - + +
15T ILE* 5.7 2.2 - - + -
80T ILE* 4.3 5.6 - - + +
84T ALA* 6.2 2.2 - - + -
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Residues in contact with ILE 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72S LEU* 2.9 25.9 + - + +
73S ILE* 3.7 5.6 - - + +
75S VAL* 1.3 78.1 - - + +
77S LYS* 1.3 62.4 + - - +
79S GLY* 3.2 1.9 + - - -
80S VAL* 3.0 24.7 + - + +
80T ILE* 3.8 20.7 - - + +
81T MET* 3.9 20.4 - - + -
84T ALA* 3.8 28.9 - - + -
60U ILE* 3.8 22.4 - - + +
61U ASN* 3.8 32.8 - - + -
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Residues in contact with LYS 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S ILE* 4.9 3.1 - - + +
49S LYS* 4.8 3.7 - - - +
54S TRP* 4.1 28.7 - - + -
57S GLU* 4.0 18.0 + - - +
73S ILE* 3.0 26.1 + - + +
74S LEU 3.8 3.1 - - - +
76S ILE* 1.3 76.5 - - - +
78S MET* 1.3 61.5 + - - +
80S VAL* 3.9 5.6 - - - +
81S ALA* 3.0 25.3 + - - +
56U LYS 5.6 3.4 + - - -
57U GLU* 5.2 4.0 + - - +
59U ASP 5.5 0.2 - - - -
60U ILE* 3.6 44.6 - - + +
62U THR* 6.2 1.6 - - - -
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Residues in contact with MET 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S GLU 4.0 9.0 - - - +
42S SER* 4.0 11.0 - - - -
43S PRO* 3.8 26.0 - - + -
45S TYR* 4.6 1.8 + - - -
46S ILE* 3.9 22.9 - - + +
74S LEU* 2.8 44.4 + - + +
75S VAL* 3.7 4.0 - - - +
77S LYS* 1.3 77.8 - - - +
79S GLY* 1.4 55.0 + - - +
81S ALA* 3.5 1.4 + - - +
82S ALA* 2.9 31.5 + - - +
8T LEU* 3.7 33.4 - - + -
9T GLU* 4.7 5.2 - - + -
12T ILE* 3.7 19.4 - - + +
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Residues in contact with GLY 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75S VAL 2.8 16.0 + - - -
76S ILE 3.2 0.2 + - - -
78S MET* 1.4 68.2 - - - +
80S VAL* 1.3 60.7 + - - +
82S ALA* 3.3 1.6 + - - +
83S HIS 2.9 25.8 + - - -
12T ILE* 3.8 20.6 - - - +
16T ILE* 4.1 0.9 - - - +
76T PHE* 3.4 16.4 - - - -
80T ILE* 3.6 17.9 - - - -
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Residues in contact with VAL 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76S ILE 3.0 17.7 + - - +
77S LYS* 3.9 5.8 - - - +
79S GLY* 1.3 76.1 - - - +
81S ALA* 1.3 62.3 + - - +
83S HIS* 3.4 2.8 + - - +
84S LYS* 3.1 24.3 + - + +
76T PHE* 3.9 7.8 - - + -
77T GLU* 3.8 26.3 - - + +
80T ILE* 4.1 19.7 - - + -
60U ILE 5.5 0.9 - - - +
61U ASN* 4.0 20.9 - - - +
62U THR* 3.8 18.6 - - - +
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Residues in contact with ALA 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45S TYR* 3.7 26.7 - - + -
46S ILE* 4.5 5.6 - - + -
77S LYS 3.0 19.2 + - - +
78S MET* 3.7 4.5 - - - +
80S VAL* 1.3 77.5 - - - +
82S ALA* 1.3 58.6 + - - +
84S LYS* 3.3 9.1 + - - +
85S LYS* 3.0 33.4 + - - +
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Residues in contact with ALA 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45S TYR* 3.6 15.9 + - - +
78S MET 2.9 17.6 + - - +
79S GLY 3.9 0.9 - - - +
81S ALA* 1.3 72.9 - - - +
83S HIS* 1.3 66.6 + - - +
85S LYS* 3.3 5.4 + - - +
86S SER* 2.9 23.2 + - - -
12T ILE* 4.0 10.8 - - + -
16T ILE* 3.6 19.4 - - + +
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Residues in contact with HIS 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79S GLY 2.9 10.8 + - - +
80S VAL 3.8 3.8 + - - +
82S ALA* 1.3 77.0 - - - +
84S LYS* 1.3 66.7 + - - +
86S SER* 2.8 22.2 + - - -
87S HIS* 3.5 13.5 - + - -
16T ILE* 3.5 12.7 - - + +
19T PHE* 4.4 0.6 - + - -
20T HIS* 3.5 14.6 - + - -
30T ASP* 2.8 18.7 + - - -
76T PHE* 3.4 58.1 - + + +
77T GLU* 4.9 11.2 + - - -
202T MN 2.1 36.5 + - - -
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Residues in contact with LYS 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80S VAL* 3.1 16.0 + - + +
81S ALA* 3.6 10.8 - - - +
83S HIS* 1.3 80.7 + - - +
85S LYS* 1.3 67.5 + - + +
87S HIS* 3.2 17.0 + - - +
88S GLU* 3.4 31.7 + - - +
77T GLU* 6.0 1.8 - - - +
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Residues in contact with LYS 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S TYR* 3.4 59.5 - - + +
81S ALA* 3.0 18.0 + - - +
82S ALA* 3.7 7.2 - - - +
83S HIS 3.3 0.2 - - - -
84S LYS* 1.3 83.6 - - + +
86S SER* 1.3 60.9 + - - +
88S GLU* 3.0 44.3 + - + +
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Residues in contact with SER 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82S ALA 2.9 13.5 + - - -
83S HIS* 2.8 20.2 + - - -
85S LYS* 1.3 77.1 - - - +
87S HIS* 1.3 70.1 + - - +
88S GLU 3.4 3.4 + - - +
16T ILE* 4.6 7.6 - - - -
20T HIS* 3.6 19.6 - - - -
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Residues in contact with HIS 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83S HIS* 3.5 16.8 - + - -
84S LYS* 3.2 8.1 + - - +
85S LYS 3.0 1.2 - - - -
86S SER* 1.3 91.6 + - - +
88S GLU* 1.3 64.2 + - - +
89S GLU* 5.0 1.6 - - - +
20T HIS* 3.1 17.4 + + - -
30T ASP* 3.9 8.7 - - + -
202T MN 2.0 37.5 + - - -
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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
------------------------------------------------------------
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