Contacts of the helix formed by residues 75 - 95 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63S ASP* 5.4 0.5 - - - +
19V PHE* 3.7 2.7 - - - -
30V ASP 4.6 0.9 - - - -
31V THR* 4.2 16.7 - - - +
69V ASN* 6.4 0.2 - - - -
73V GLN* 3.9 1.4 + - - +
74V LEU* 1.3 76.3 - - - +
76V PHE* 1.3 59.7 + - - +
77V GLU* 3.5 17.8 + - - +
78V GLU* 3.0 36.0 + - - +
79V PHE* 2.9 26.7 + - - +
203V CA 4.4 0.4 - - - -
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Residues in contact with PHE 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79U GLY* 3.2 31.0 - - - -
80U VAL* 4.0 7.6 - - - -
83U HIS* 3.4 44.1 - + + +
12V ILE* 5.5 0.4 - - + -
15V ILE* 3.9 22.9 - - + -
16V ILE* 3.7 31.6 - - + -
19V PHE* 3.3 38.7 - + + -
30V ASP 4.6 1.8 + - - -
75V SER* 1.3 74.5 - - - +
77V GLU* 1.3 61.6 + - - +
79V PHE* 3.2 5.3 + + - -
80V ILE* 2.9 51.9 + - + +
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Residues in contact with GLU 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61S ASN* 2.8 43.8 + - - +
62S THR* 3.9 11.7 + - - +
63S ASP* 4.3 10.1 - - + -
80U VAL* 3.8 32.4 - - + +
83U HIS* 4.8 10.8 + - - -
84U LYS* 5.6 6.1 - - - +
75V SER* 3.7 18.6 - - - +
76V PHE* 1.3 83.9 + - - +
78V GLU* 1.3 61.9 + - - +
80V ILE* 3.2 14.4 - - - +
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Residues in contact with GLU 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61S ASN* 4.1 5.2 - - - +
63S ASP* 4.1 11.0 - - + +
66V LEU* 3.2 37.9 - - - +
67V ASP* 4.0 0.7 - - - -
68V THR* 3.1 24.7 + - - +
69V ASN* 3.1 18.1 + - - +
73V GLN 3.0 5.2 - - - +
74V LEU* 3.2 6.4 - - + +
75V SER* 3.0 31.9 + - - +
77V GLU* 1.3 78.1 - - - +
79V PHE* 1.3 63.5 + - - +
81V MET* 3.3 20.3 + - - +
203V CA 2.4 30.0 - - - -
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Residues in contact with PHE 79 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5U LEU* 5.1 2.2 - - + -
15V ILE* 4.1 12.1 - - + -
18V THR* 6.2 0.2 - - - -
19V PHE* 3.6 31.6 - + + -
32V LEU* 3.8 15.7 - - + -
37V PHE* 4.4 18.8 - + - -
40V LEU* 3.9 36.6 - - + -
66V LEU* 5.2 1.1 - - - -
74V LEU* 4.5 11.6 - - + +
75V SER 2.9 17.4 + - - +
76V PHE* 3.2 12.5 + + - +
78V GLU* 1.3 74.2 - - - +
80V ILE* 1.3 68.0 + - - +
82V LEU* 2.9 26.1 + - + +
83V MET* 3.4 44.8 + - + -
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Residues in contact with ILE 80 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61S ASN* 4.4 1.8 - - + -
75U VAL* 4.2 6.3 - - + +
76U ILE* 3.7 34.0 - - + +
79U GLY* 3.6 31.2 - - - -
80U VAL* 4.1 14.4 - - + -
12V ILE* 6.3 0.7 - - + -
15V ILE* 5.1 7.4 - - + -
76V PHE* 2.9 33.4 + - + +
77V GLU 3.2 20.2 - - - +
79V PHE* 1.3 80.6 - - - +
81V MET* 1.3 57.9 + - - +
82V LEU 3.2 0.2 - - - -
83V MET* 3.2 17.5 + - + -
84V ALA* 2.9 27.4 + - - +
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Residues in contact with MET 81 (chain V).
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 1.3 - - + -
61S ASN* 3.4 45.1 - - + +
67S ASN* 3.2 22.9 - - - +
69S GLN* 3.2 32.1 - - - +
70S GLU* 3.6 16.8 - - + +
101S CA 4.4 0.2 - - - -
76U ILE* 4.1 21.1 - - + -
66V LEU* 4.3 6.1 - - + -
78V GLU* 3.3 14.0 + - - +
79V PHE 3.0 0.4 + - - -
80V ILE* 1.3 82.0 - - - +
82V LEU* 1.3 55.3 + - - +
84V ALA* 3.5 5.2 + - - +
85V ARG* 3.0 44.2 + - - +
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Residues in contact with LEU 82 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V PHE* 3.8 34.8 - - + -
45V LEU* 4.2 14.6 - - + -
49V LEU* 4.6 9.6 - - + -
62V ILE* 4.3 17.5 - - + -
66V LEU* 3.8 19.8 - - + +
79V PHE* 2.9 14.7 + - + +
81V MET* 1.3 74.4 - - - +
83V MET* 1.3 80.2 + - + +
85V ARG* 3.3 12.0 + - + +
86V LEU* 2.9 47.2 + - + +
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Residues in contact with MET 83 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U LEU* 4.0 28.5 - - + -
9U LEU* 4.1 18.7 - - + +
15V ILE* 3.7 26.5 - - + -
45V LEU* 4.0 20.6 - - + -
79V PHE* 3.7 39.7 - - + +
80V ILE* 3.2 16.3 + - + +
82V LEU* 1.3 96.2 - - + +
84V ALA* 1.3 53.7 - - - +
86V LEU* 3.9 7.2 - - + +
87V THR* 2.8 38.1 + - - -
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Residues in contact with ALA 84 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69S GLN* 6.2 0.2 - - - +
72U LEU* 3.7 22.0 - - + +
75U VAL* 6.3 2.2 - - + -
76U ILE* 3.6 34.3 - - + -
80V ILE* 2.9 14.4 + - + +
81V MET* 3.9 7.2 - - - +
83V MET* 1.3 76.7 - - - +
85V ARG* 1.3 63.6 + - + +
87V THR* 3.4 5.5 + - - -
88V TRP* 3.0 24.7 + - - +
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Residues in contact with ARG 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67S ASN* 3.7 9.9 - - - +
69S GLN* 3.2 36.9 + - + +
88T TRP* 4.5 16.8 - - + -
92T GLU* 5.7 2.2 - - - -
205T GOL 3.1 18.3 + - - -
62V ILE* 6.0 1.6 - - - +
65V ASP* 2.9 29.3 + - - -
66V LEU* 3.7 19.7 - - - +
81V MET* 3.0 34.8 + - - +
82V LEU* 3.3 14.9 + - + +
84V ALA* 1.3 78.2 - - + +
86V LEU* 1.3 60.2 + - + +
88V TRP* 3.4 10.2 + - + +
89V ALA* 2.8 28.4 + - - +
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Residues in contact with LEU 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U LEU* 4.0 11.7 - - + -
45V LEU* 3.7 39.7 - - + -
48V PHE* 4.2 13.3 - - + -
49V LEU* 3.9 27.1 - - + -
82V LEU* 2.9 38.3 + - + +
83V MET* 3.9 8.5 - - + +
85V ARG* 1.3 76.5 - - + +
87V THR* 1.3 61.9 + - - +
89V ALA* 3.7 7.0 - - + +
90V SER* 2.8 30.1 + - - -
109V LEU* 4.0 13.7 - - + +
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Residues in contact with THR 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U LEU* 3.5 46.6 - - - +
12U ILE* 4.0 17.5 - - + +
13U ILE* 3.6 10.2 - - + +
68U PHE* 3.7 23.3 - - + -
72U LEU* 4.1 7.4 - - + -
83V MET 2.8 23.1 + - - -
84V ALA* 3.7 5.1 - - - -
86V LEU* 1.3 73.5 - - - +
88V TRP* 1.3 66.1 + - - +
90V SER* 3.2 3.7 + - - -
91V HIS* 3.0 21.7 + - - +
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Residues in contact with TRP 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85T ARG* 4.4 23.1 - - + -
88T TRP* 4.0 32.2 - + - +
68U PHE* 3.9 22.7 - + + -
69U GLN* 3.2 55.9 - - + -
72U LEU* 3.9 12.0 - - + +
84V ALA 3.0 16.9 + - - +
85V ARG* 3.4 10.3 - - + +
87V THR* 1.3 79.3 - - - +
89V ALA* 1.3 61.5 + - + +
91V HIS* 3.3 4.8 + + - +
92V GLU* 2.9 72.1 + - + +
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Residues in contact with ALA 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85V ARG 2.8 18.0 + - - +
86V LEU* 3.7 9.6 - - + +
87V THR 3.2 0.2 - - - -
88V TRP* 1.3 79.5 - - + +
90V SER* 1.3 59.8 + - - +
92V GLU* 3.4 7.5 + - - +
93V LYS* 2.9 27.5 + - - +
109V LEU* 4.0 21.7 - - + +
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Residues in contact with SER 90 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10U ASN* 2.7 28.2 + - - -
13U ILE* 3.9 4.3 - - - -
48V PHE* 4.0 6.4 - - - -
86V LEU 2.8 16.5 + - - -
87V THR* 3.2 6.3 + - - -
89V ALA* 1.3 76.7 - - - +
91V HIS* 1.3 58.0 + - - +
93V LYS* 3.1 4.7 + - - +
94V MET* 3.0 32.2 + - - +
108V GLY* 3.5 4.9 - - - -
109V LEU* 3.0 34.2 + - - +
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Residues in contact with HIS 91 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U ILE* 3.5 18.9 - - + +
17U HIS* 3.2 14.0 - + - -
27U HIS* 3.3 24.0 - + - -
68U PHE* 3.6 32.9 - + + +
87V THR 3.0 16.3 + - - +
88V TRP* 3.7 6.6 - + - +
90V SER* 1.3 73.8 - - - +
92V GLU* 1.3 73.2 + - - +
94V MET* 3.2 14.5 + - - +
95V HIS* 3.2 19.9 + + - -
105V HIS* 3.4 12.8 - + - -
201V MN 2.3 35.5 + - - -
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Residues in contact with GLU 92 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85T ARG* 6.0 1.1 - - - -
88V TRP* 2.9 70.8 + - + +
89V ALA* 3.5 8.3 - - - +
91V HIS* 1.3 83.0 + - - +
93V LYS* 1.3 62.1 + - - +
95V HIS* 3.0 16.8 + - - +
96V GLU* 3.0 17.4 + - - +
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Residues in contact with LYS 93 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89V ALA 2.9 14.0 + - - +
90V SER 3.1 9.2 + - - +
92V GLU* 1.3 74.6 - - - +
94V MET* 1.3 62.7 + - - +
95V HIS 3.2 0.7 + - - -
96V GLU* 3.2 23.9 + - + +
106V LYS* 4.4 6.2 - - - +
107V PRO 3.8 8.0 - - - +
108V GLY 3.7 23.8 + - - +
109V LEU* 3.9 23.0 - - + +
110V GLY 5.2 3.0 - - - +
111V GLU* 5.6 2.8 + - - +
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Residues in contact with MET 94 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10U ASN* 3.7 23.1 - - + +
13U ILE* 3.5 35.9 - - + -
14U ASP* 5.7 2.5 - - - +
90V SER* 3.0 18.6 + - - +
91V HIS* 3.2 9.6 + - - +
93V LYS* 1.3 77.4 - - - +
95V HIS* 1.3 58.5 + - - +
98V ASP* 5.4 0.3 - - - +
104V HIS 3.9 2.3 - - - +
105V HIS* 3.6 45.1 - - + -
106V LYS* 2.8 53.7 + - - +
107V PRO 3.8 1.3 - - - -
108V GLY* 3.8 12.6 - - - +
112V GLY 5.6 0.4 - - - +
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Residues in contact with HIS 95 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61T HIS* 3.8 16.7 + + - +
27U HIS* 3.2 13.5 + + - -
91V HIS* 3.2 37.5 + + - +
92V GLU* 3.0 12.8 + - - +
94V MET* 1.3 76.5 - - - +
96V GLU* 1.3 65.3 + - - +
97V GLY 3.2 0.9 + - - -
98V ASP* 2.8 44.2 + - + +
103V HIS* 3.6 11.4 - + - -
104V HIS 3.1 20.1 + - - -
105V HIS* 3.3 5.2 - + - -
106V LYS* 5.5 0.4 - - - -
201V MN 2.3 29.7 + - - -
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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
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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