Contacts of the helix formed by residues 93 - 112 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LYS* 1.3 76.8 - - - +
94B ALA* 1.3 79.2 + - + +
95B HIS* 2.9 43.4 + - + +
96B ASP* 3.0 16.4 + - - +
97B ALA* 3.1 8.3 + - - -
311B GLY 4.5 1.1 - - - +
313B SER* 3.9 20.9 - - - -
315B ASP 4.4 1.3 - - - +
316B SER* 3.6 31.4 - - - -
317B GLY 3.7 4.0 - - - +
318B ASN* 3.3 26.2 - - + +
320B PHE* 3.8 30.7 - - - -
321B GLY* 3.9 4.7 - - - +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B CYS* 4.3 10.4 + - + -
92B LYS 3.9 0.8 + - - -
93B ILE* 1.3 73.3 - - + +
95B HIS* 1.3 59.1 + - - +
97B ALA* 3.0 9.2 + - - +
98B MET* 2.8 35.2 + - + +
313B SER* 4.9 7.3 + - - +
316B SER* 3.8 22.0 - - - +
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Residues in contact with HIS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 2.9 39.7 + - + +
94B ALA* 1.3 77.6 - - - +
96B ASP* 1.3 87.8 + - - -
98B MET* 3.8 7.0 - - - +
99B GLY* 3.0 24.6 + - - -
317B GLY* 5.4 1.2 + - - -
318B ASN 3.3 14.1 - - - -
319B ASP* 3.3 21.7 + - - -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LYS* 3.9 18.9 + - + +
93B ILE 3.0 9.9 + - - +
95B HIS* 1.3 102.0 + - - +
97B ALA* 1.3 58.2 + - - +
99B GLY* 3.2 1.9 + - - -
100B GLU* 2.9 27.9 + - - +
150B PHE* 5.8 0.2 - - - -
274B GLY* 4.5 3.3 - - - -
275B SER* 3.2 45.8 + - - +
279B ARG* 3.9 8.8 + - - -
319B ASP 3.6 9.0 - - - +
320B PHE* 4.6 3.8 - - - -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B CYS* 3.6 37.0 - - + +
86B ILE* 4.1 12.5 - - + +
92B LYS* 3.7 19.8 - - + +
93B ILE 3.1 9.6 + - - +
94B ALA* 3.0 11.3 + - - +
96B ASP* 1.3 74.1 - - - +
98B MET* 1.3 59.4 + - - +
100B GLU* 3.3 6.5 - - - +
101B LEU* 2.9 28.1 + - - +
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Residues in contact with MET 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA* 4.0 26.7 - - + +
80B ASP* 5.5 3.8 - - - +
83B CYS* 3.3 22.9 - - - -
94B ALA* 2.8 22.1 + - + +
95B HIS* 3.8 8.1 - - - +
97B ALA* 1.3 69.7 - - - +
99B GLY* 1.3 56.1 + - - +
101B LEU* 3.1 10.1 + - + +
102B GLN* 2.7 55.0 + - - +
105B ILE* 6.3 1.1 - - + -
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B HIS 3.0 15.9 + - - -
96B ASP* 3.2 4.2 + - - -
97B ALA 3.2 0.2 - - - -
98B MET* 1.3 74.9 - - - +
100B GLU* 1.3 63.6 + - - +
102B GLN* 3.3 7.4 + - - +
103B ARG* 3.1 35.2 + - - +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 4.0 8.3 - - + +
92B LYS* 3.0 28.5 + - - +
96B ASP 2.9 12.9 + - - +
97B ALA 3.3 9.0 - - - +
99B GLY* 1.3 76.3 - - - +
101B LEU* 1.3 63.9 + - - +
103B ARG* 3.4 1.8 + - - +
104B GLY* 3.0 17.3 + - - -
150B PHE* 3.1 29.1 - - + -
151B PRO* 3.2 7.5 - - - +
152B VAL* 2.6 40.7 + - + -
153B MET* 3.0 35.7 + - + +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 4.0 13.9 - - + +
79B ALA* 3.6 44.4 - - + +
82B ILE* 4.3 24.2 - - + -
83B CYS* 4.3 3.4 - - - -
86B ILE* 5.3 0.9 - - + -
97B ALA 2.9 14.9 + - - +
98B MET* 3.4 18.2 - - + +
100B GLU* 1.3 76.1 - - - +
102B GLN* 1.3 56.6 + - - +
104B GLY* 3.1 2.4 + - - -
105B ILE* 2.9 48.6 + - + +
152B VAL* 4.0 24.2 - - + -
156B LEU* 5.0 1.6 - - + -
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 5.2 5.3 + - - +
98B MET* 2.7 37.4 + - - +
99B GLY* 3.5 9.2 - - - +
101B LEU* 1.3 69.7 - - - +
103B ARG* 1.3 61.1 + - + +
105B ILE* 3.2 22.0 + - - +
106B GLU* 2.9 42.1 + - - +
66D ARG* 4.0 26.1 - - - +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY 3.1 20.9 + - - +
100B GLU* 3.9 0.6 - - - +
102B GLN* 1.3 76.3 - - + +
104B GLY* 1.3 61.7 + - - +
106B GLU* 3.2 28.5 + - - +
107B ASN* 2.9 21.0 + - - +
150B PHE* 4.5 12.9 - - - -
153B MET* 3.3 46.2 - - - +
157B TRP* 5.4 0.4 - - - -
279B ARG* 5.7 6.3 - - - +
440B LEU* 6.2 2.2 - - - +
442B VAL* 3.9 40.2 - - - +
443B PRO 5.4 3.1 + - - -
444B VAL* 6.4 1.3 - - - +
445B ALA* 5.1 0.2 - - - +
449B PHE* 5.9 0.4 - - - -
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLU 3.0 14.5 + - - -
101B LEU 3.1 4.2 + - - -
103B ARG* 1.3 77.0 - - - +
105B ILE* 1.3 60.4 + - - +
107B ASN* 3.2 22.1 + - - +
108B VAL* 3.2 14.9 + - - +
153B MET* 3.9 6.5 - - - +
156B LEU* 3.6 29.3 - - - +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 3.7 30.5 - - + +
75B LEU* 3.9 28.7 - - + -
76B GLU* 3.8 33.7 - - + +
79B ALA* 6.2 0.2 - - + -
98B MET* 6.3 1.3 - - + -
101B LEU* 2.9 37.0 + - + +
102B GLN* 3.6 22.2 - - - +
104B GLY* 1.3 72.5 - - - +
106B GLU* 1.3 61.1 + - - +
108B VAL* 3.0 10.1 + - - +
109B GLU* 2.7 33.5 + - - +
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN* 2.9 27.5 + - + +
103B ARG* 3.4 26.4 - - - +
104B GLY 3.2 0.4 - - - -
105B ILE* 1.3 77.2 - - - +
107B ASN* 1.3 59.5 + - - +
109B GLU* 3.3 22.6 + - - +
110B TYR* 3.1 15.6 + - - +
444B VAL* 3.9 18.3 - - + +
445B ALA* 3.0 24.5 + - + +
62D LEU* 4.4 14.7 - - + +
66D ARG* 3.3 25.7 + - - +
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Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG 2.9 18.8 - - - +
104B GLY* 3.2 11.4 + - - +
105B ILE 3.2 0.4 - - - -
106B GLU* 1.3 73.2 - - - +
108B VAL* 1.3 61.0 + - - +
110B TYR* 3.2 5.4 + - - +
111B ALA* 2.9 28.1 + - - +
156B LEU 3.2 25.2 - - - +
157B TRP* 3.4 21.4 + - - -
160B PRO* 4.7 2.5 - - + +
161B MET* 5.4 1.6 - - - +
445B ALA* 3.7 12.8 + - - +
463B TYR* 3.4 42.8 - - + +
464B GLY 5.0 0.2 - - - +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 3.4 36.8 - - + +
71B PHE* 4.0 5.4 - - + -
72B LYS* 4.0 20.2 - - + +
75B LEU* 4.0 13.5 - - + -
104B GLY 3.5 12.8 - - - +
105B ILE* 3.0 10.2 + - - +
107B ASN* 1.3 78.2 - - - +
109B GLU* 1.3 62.1 + - - +
111B ALA* 3.1 8.7 + - - +
112B CYS* 3.1 21.2 + - - -
156B LEU* 3.9 22.9 - - + -
160B PRO* 4.0 11.4 - - + -
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 3.2 38.9 + - + -
105B ILE* 2.7 24.3 + - - +
106B GLU* 3.5 14.6 - - - +
107B ASN 3.2 0.2 - - - -
108B VAL* 1.3 72.3 - - - +
110B TYR* 1.3 63.2 + - - +
112B CYS* 3.2 20.4 + - - +
113B GLY 3.9 1.9 + - - -
62D LEU* 3.3 21.4 - - + +
66D ARG* 2.6 39.5 + - - +
69D PHE* 3.8 23.9 - - + -
112D CYS 5.5 1.8 - - - +
113D GLY* 5.8 4.0 - - - -
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Residues in contact with TYR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU 3.1 11.3 + - - +
107B ASN* 3.2 7.8 + - - +
109B GLU* 1.3 78.3 - - - +
111B ALA* 1.3 62.8 + - - +
113B GLY* 3.1 15.2 + - - -
117B LEU* 3.2 39.7 - - + +
161B MET* 3.4 20.2 - - + -
445B ALA* 3.4 19.7 - - + +
446B TYR* 3.3 32.8 - + + -
464B GLY* 3.6 24.9 - - - -
465B PRO* 3.4 21.9 - - + +
116D GLU* 3.0 37.2 + - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 4.1 12.8 - - + -
107B ASN 2.9 13.9 + - - +
108B VAL* 3.1 13.4 + - - +
110B TYR* 1.3 79.0 - - - +
112B CYS* 1.3 61.0 + - - +
114B ALA* 3.1 23.3 + - - +
160B PRO 4.1 26.9 - - - +
161B MET* 4.3 14.6 - - + +
164B VAL* 3.6 12.5 - - + +
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Residues in contact with CYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 3.4 25.8 - - - +
68B MET* 3.7 8.5 - - - +
69B PHE* 3.6 68.5 - - + -
72B LYS* 5.2 1.1 - - - -
108B VAL* 3.1 21.0 + - - -
109B GLU* 3.2 13.9 - - - +
110B TYR 3.2 0.6 - - - -
111B ALA* 1.3 76.0 - - - +
113B GLY* 1.3 53.7 + - - +
114B ALA 3.3 1.4 + - - -
115B PRO* 4.1 3.1 - - - +
69D PHE* 4.1 11.0 - - + -
109D GLU 6.1 0.2 - - - -
112D CYS* 6.0 0.4 - - + -
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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