Contacts of the helix formed by residues 93 - 113 (chain G) in PDB entry 4ZZ7
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 ILE 93 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83G CYS 5.8 0.2 - - - -
91G GLY 4.7 1.1 - - - +
92G LYS* 1.3 77.5 - - - +
94G ALA* 1.3 81.2 + - + +
95G HIS* 3.0 43.9 + - + +
96G ASP* 3.1 15.3 + - - +
97G ALA* 3.2 10.3 + - - +
311G GLY 4.6 3.1 - - - +
313G SER* 4.1 16.4 - - - -
315G ASP 4.8 0.9 - - - +
316G SER* 3.9 12.1 - - - -
317G GLY 3.9 17.9 - - - +
318G ASN* 3.5 25.4 - - + +
320G PHE* 3.8 34.1 - - - -
321G GLY* 3.8 4.5 - - - +
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Residues in contact with ALA 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G CYS* 4.5 10.0 + - + -
92G LYS 4.1 0.2 + - - -
93G ILE* 1.3 76.1 - - + +
95G HIS* 1.3 57.3 + - - +
97G ALA* 3.2 7.6 + - - +
98G MET* 2.8 37.2 + - + +
313G SER* 4.9 6.9 + - - +
316G SER* 3.9 21.3 - - - +
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Residues in contact with HIS 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G ILE* 3.0 26.6 + - + +
94G ALA* 1.3 76.4 - - - +
96G ASP* 1.3 87.2 + - - +
98G MET* 3.8 5.8 - - - +
99G GLY* 2.9 24.1 + - - -
317G GLY* 5.5 1.0 + - - -
318G ASN 3.3 24.7 + - - -
319G ASP* 3.5 20.1 + - - -
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Residues in contact with ASP 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G LYS* 4.0 17.4 + - + +
93G ILE* 3.1 11.4 + - - +
95G HIS* 1.3 100.0 + - - +
97G ALA* 1.3 57.2 + - - +
99G GLY* 3.2 2.0 + - - -
100G GLU* 2.8 34.7 + - - +
274G GLY* 4.6 2.9 - - - -
275G SER* 3.2 45.7 + - - +
279G ARG* 4.1 8.5 + - - -
319G ASP 4.0 8.0 - - - +
320G PHE* 4.8 3.5 - - - +
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Residues in contact with ALA 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G CYS* 3.6 37.2 - - + +
86G ILE* 4.1 18.9 - - + +
92G LYS* 3.9 11.8 - - + +
93G ILE 3.2 10.0 + - - +
94G ALA* 3.5 8.5 - - - +
96G ASP* 1.3 79.4 - - - +
98G MET* 1.3 57.5 + - - +
100G GLU* 3.1 6.9 + - - +
101G LEU* 2.9 27.5 + - - +
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Residues in contact with MET 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G ALA* 3.9 25.1 - - + +
80G ASP* 5.2 4.5 - - - +
83G CYS* 3.5 23.8 - - + -
94G ALA* 2.8 22.3 + - + +
95G HIS* 3.9 6.5 - - - +
97G ALA* 1.3 74.1 - - - +
99G GLY* 1.3 56.6 - - - +
101G LEU* 3.7 8.9 - - + +
102G GLN* 2.9 50.9 + - + +
105G ILE* 6.1 1.3 - - + -
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Residues in contact with GLY 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G HIS 2.9 17.7 + - - -
96G ASP* 3.2 4.9 + - - -
98G MET* 1.3 76.6 - - - +
100G GLU* 1.3 60.1 + - - +
102G GLN* 3.9 5.5 - - - +
103G ARG* 3.3 34.1 + - - +
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Residues in contact with GLU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G ILE* 4.0 8.1 - - - +
92G LYS* 2.8 29.4 + - - +
96G ASP 2.8 17.0 + - - +
97G ALA 3.1 8.5 + - - +
99G GLY* 1.3 71.4 - - - +
101G LEU* 1.3 64.2 + - - +
103G ARG* 3.6 2.0 + - - +
104G GLY* 3.2 16.8 + - - -
150G PHE* 3.1 31.5 - - + -
151G PRO* 3.2 6.9 - - - +
152G VAL* 2.8 38.1 + - + -
153G MET* 3.0 32.4 + - + +
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Residues in contact with LEU 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G LEU* 3.9 16.8 - - + +
79G ALA* 3.6 44.0 - - + +
82G ILE* 4.1 24.9 - - + -
83G CYS* 4.3 5.4 - - - -
86G ILE* 5.3 1.1 - - + +
97G ALA 2.9 15.2 + - - +
98G MET* 3.3 9.2 + - + +
100G GLU* 1.3 74.5 - - - +
102G GLN* 1.3 61.3 + - - +
104G GLY* 3.3 1.0 + - - -
105G ILE* 2.8 51.5 + - + +
152G VAL* 3.8 26.2 - - + -
156G LEU* 4.9 2.0 - - + -
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Residues in contact with GLN 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ARG* 4.1 27.0 - - - +
76G GLU* 4.9 5.7 + - - +
98G MET* 2.9 36.4 + - + +
99G GLY* 3.9 7.2 - - - +
100G GLU 3.3 0.2 - - - -
101G LEU* 1.3 77.2 - - - +
103G ARG* 1.3 59.5 + - + +
105G ILE* 3.0 23.9 + - - +
106G GLU* 2.9 39.7 + - - +
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Residues in contact with ARG 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G GLY 3.3 21.3 + - - +
100G GLU* 4.0 1.5 - - - +
101G LEU 3.3 0.2 - - - -
102G GLN* 1.3 78.2 - - + +
104G GLY* 1.3 60.0 + - - +
106G GLU* 3.4 20.9 + - - +
107G ASN* 3.0 24.9 + - - +
150G PHE* 4.7 10.5 - - - -
153G MET* 3.2 45.5 - - - +
157G TRP* 5.3 0.4 - - - -
279G ARG* 5.9 4.9 - - - +
440G LEU* 5.9 4.9 - - - +
442G VAL* 3.8 41.7 - - - +
443G PRO 5.5 3.1 - - - -
445G ALA* 5.1 0.5 - - - +
449G PHE* 6.0 0.6 - - - -
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Residues in contact with GLY 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G GLU 3.2 13.9 + - - -
101G LEU 3.6 2.0 - - - -
103G ARG* 1.3 75.1 - - - +
105G ILE* 1.3 64.4 + - - +
107G ASN* 3.0 27.0 + - - +
108G VAL* 3.3 10.0 + - - +
153G MET* 3.9 7.0 - - - +
156G LEU* 3.6 29.8 - - - +
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Residues in contact with ILE 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G LYS* 4.1 15.5 - - + -
75G LEU* 4.0 27.1 - - + -
76G GLU* 4.0 36.8 - - + +
79G ALA* 6.1 0.4 - - + -
98G MET* 6.1 1.8 - - + -
101G LEU* 2.8 40.4 + - + +
102G GLN* 3.0 25.1 + - - +
104G GLY* 1.3 75.2 - - - +
106G GLU* 1.3 59.5 + - - +
108G VAL* 2.9 12.0 + - - +
109G GLU* 2.9 38.6 + - - +
156G LEU* 4.3 0.2 - - - +
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Residues in contact with GLU 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E LEU* 3.8 16.9 - - + +
66E ARG* 3.1 27.3 + - - +
102G GLN* 2.9 26.3 + - + +
103G ARG* 3.5 22.6 - - - +
105G ILE* 1.3 76.4 - - - +
107G ASN* 1.3 55.4 + - - +
109G GLU* 3.5 20.9 + - - +
110G TYR* 3.1 19.6 + - - +
444G VAL* 3.6 22.5 - - - +
445G ALA* 2.9 24.8 + - + +
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Residues in contact with ASN 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G ARG 3.0 18.0 + - - +
104G GLY* 3.0 14.3 + - - +
106G GLU* 1.3 75.1 - - - +
108G VAL* 1.3 60.1 + - - +
110G TYR* 3.7 4.8 + - - +
111G ALA* 3.2 24.1 + - - +
156G LEU 3.3 22.6 - - - +
157G TRP* 3.4 22.9 + - - -
160G PRO* 4.4 3.8 - - - +
161G MET* 5.3 2.9 + - - +
445G ALA* 3.8 12.8 + - - +
463G TYR* 3.4 42.2 - - + +
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Residues in contact with VAL 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G MET* 3.3 44.6 - - + +
71G PHE* 3.8 13.7 - - + -
72G LYS* 4.0 17.0 - - + +
75G LEU* 3.8 23.8 - - + -
104G GLY 3.7 12.3 - - - +
105G ILE* 2.9 9.0 + - - +
107G ASN* 1.3 75.8 - - - +
109G GLU* 1.3 60.6 + - - +
111G ALA* 3.0 8.2 + - - +
112G CYS* 3.0 26.8 + - - -
156G LEU* 4.1 8.3 - - + -
160G PRO* 4.3 3.6 - - + -
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Residues in contact with GLU 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E LEU* 3.3 20.9 - - + +
66E ARG* 2.4 39.0 + - - +
69E PHE* 3.8 26.7 - - + -
112E CYS 5.6 1.4 - - - +
113E GLY* 5.8 3.3 - - - -
72G LYS* 3.0 38.1 + - + -
76G GLU* 4.7 0.5 - - - +
105G ILE* 2.9 16.8 + - - +
106G GLU* 3.6 19.6 - - - +
108G VAL* 1.3 74.8 - - - +
110G TYR* 1.3 63.3 + - - +
112G CYS* 3.1 20.6 + - - +
113G GLY 3.8 2.4 + - - -
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Residues in contact with TYR 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E PRO* 6.3 0.2 - - + -
116E GLU* 3.0 35.1 + - + -
106G GLU 3.1 12.8 + - - +
107G ASN* 3.9 4.9 - - - +
108G VAL 3.3 0.2 - - - -
109G GLU* 1.3 80.7 - - - +
111G ALA* 1.3 59.6 + - - +
113G GLY* 3.3 11.1 + - - -
117G LEU* 3.1 45.3 - - + +
161G MET* 3.5 24.9 - - + -
445G ALA* 3.2 21.1 - - + +
446G TYR* 3.3 37.2 - + + -
464G GLY* 3.7 18.8 - - - -
465G PRO* 3.7 19.8 - - + +
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Residues in contact with ALA 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G MET* 4.2 10.8 - - + -
107G ASN 3.2 14.7 + - - +
108G VAL* 3.0 14.9 + - - +
110G TYR* 1.3 73.0 - - - +
112G CYS* 1.3 64.4 + - - +
113G GLY 3.1 2.7 + - - -
114G ALA* 3.3 21.0 + - - +
117G LEU* 5.3 0.2 - - - -
160G PRO 3.9 28.0 - - - +
161G MET* 4.2 13.0 - - + +
164G VAL* 3.5 12.7 - - + +
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Residues in contact with CYS 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E PHE* 4.1 11.4 - - + -
109E GLU 5.5 0.9 - - - +
112E CYS* 5.9 0.4 - - + -
65G ALA* 3.4 23.3 - - - +
68G MET* 3.7 7.4 - - - -
69G PHE* 3.5 68.7 - - + -
72G LYS* 5.2 1.6 - - - -
108G VAL* 3.0 27.6 + - - -
109G GLU* 3.1 11.4 + - - +
111G ALA* 1.3 77.2 - - - +
113G GLY* 1.3 55.0 + - - +
114G ALA 3.2 4.0 + - - -
115G PRO* 4.1 3.3 - - - +
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Residues in contact with GLY 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E GLU 5.9 2.5 - - - -
113E GLY* 5.5 11.4 - - - -
109G GLU 3.8 3.2 + - - -
110G TYR 3.3 13.8 + - - -
111G ALA 3.1 1.4 - - - -
112G CYS* 1.3 75.7 - - - +
114G ALA* 1.3 62.6 + - - -
115G PRO* 3.4 6.3 - - - -
116G GLU* 3.3 19.1 + - - +
117G LEU* 3.3 15.2 + - - +
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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