Contacts of the helix formed by residues 93 - 112 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H LYS* 1.3 79.7 - - - +
94H ALA* 1.3 77.6 + - + +
95H HIS* 3.3 33.4 - - + +
96H ASP* 2.9 18.8 + - - +
97H ALA* 3.3 5.3 + - - -
311H GLY 4.4 1.1 - - - +
313H SER* 3.7 22.7 - - - -
316H SER* 3.7 12.6 - - - -
317H GLY 3.5 20.6 - - - +
318H ASN* 3.2 34.3 - - + +
320H PHE* 3.7 32.5 - - - +
321H GLY* 3.8 5.1 - - - +
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Residues in contact with ALA 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H CYS* 4.5 9.3 - - + -
92H LYS 4.0 0.4 + - - -
93H ILE* 1.3 81.1 - - + +
95H HIS* 1.3 58.3 + - - +
97H ALA* 3.3 7.0 + - - +
98H MET* 2.8 35.8 + - + +
313H SER* 4.7 8.4 + - - +
316H SER* 4.6 14.8 - - - +
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Residues in contact with HIS 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H ILE* 3.0 39.8 + - + +
94H ALA* 1.3 77.3 - - - +
96H ASP* 1.3 83.9 + - - +
98H MET* 3.9 6.4 - - - +
99H GLY* 3.0 25.1 + - - -
317H GLY* 5.4 1.6 + - - -
318H ASN 3.4 13.2 - - - -
319H ASP* 3.5 21.3 + - - -
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Residues in contact with ASP 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H LYS* 3.9 20.8 + - + +
93H ILE 2.9 11.3 + - - +
95H HIS* 1.3 100.3 + - - +
97H ALA* 1.3 57.0 + - - +
99H GLY* 3.5 1.4 + - - -
100H GLU* 3.0 26.9 + - - +
150H PHE* 5.9 0.2 - - - -
274H GLY* 4.7 2.6 - - - -
275H SER* 3.1 44.9 + - - +
279H ARG* 4.3 6.2 + - - -
319H ASP 3.9 12.3 - - - +
320H PHE* 4.5 4.9 - - - +
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Residues in contact with ALA 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H CYS* 3.7 35.0 - - + +
86H ILE* 4.1 17.8 - - + +
92H LYS* 3.8 17.4 - - + +
93H ILE 3.3 6.3 + - - +
94H ALA* 3.3 9.3 + - - +
96H ASP* 1.3 78.0 - - - +
98H MET* 1.3 60.1 + - - +
100H GLU* 3.6 4.7 - - - +
101H LEU* 2.9 28.9 + - - +
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Residues in contact with MET 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ALA* 4.0 24.2 - - + +
80H ASP* 5.4 4.7 - - - +
83H CYS* 3.5 21.5 - - + -
94H ALA* 2.8 24.3 + - + +
95H HIS* 3.9 7.6 - - - +
97H ALA* 1.3 71.0 - - - +
99H GLY* 1.3 57.9 + - - +
101H LEU* 3.2 8.9 + - + +
102H GLN* 2.9 46.7 + - + +
105H ILE* 6.2 0.2 - - + -
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Residues in contact with GLY 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H HIS 3.0 17.9 + - - -
96H ASP* 3.8 1.8 - - - -
97H ALA 3.2 0.2 - - - -
98H MET* 1.3 72.7 - - - +
100H GLU* 1.3 64.6 + - - +
102H GLN* 3.3 6.0 + - - +
103H ARG* 3.1 33.4 + - - +
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Residues in contact with GLU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H ILE* 3.9 11.3 - - + +
92H LYS* 2.9 26.8 + - - +
96H ASP 3.0 16.7 + - - +
97H ALA 3.6 4.7 - - - +
99H GLY* 1.3 74.6 - - - +
101H LEU* 1.3 64.1 + - - +
102H GLN 3.2 0.5 + - - -
103H ARG* 3.2 5.8 + - - +
104H GLY* 3.1 17.7 + - - -
150H PHE* 3.1 32.2 - - + -
151H PRO* 3.2 4.5 - - - +
152H VAL* 2.8 36.5 + - + -
153H MET* 3.1 35.6 + - + +
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Residues in contact with LEU 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H LEU* 4.0 21.8 - - + +
79H ALA* 3.7 43.3 - - + +
82H ILE* 4.1 22.4 - - + -
83H CYS* 4.2 6.3 - - - -
86H ILE* 5.5 0.7 - - + -
97H ALA 2.9 19.5 + - - +
98H MET* 3.2 10.5 + - + +
100H GLU* 1.3 76.4 - - - +
102H GLN* 1.3 57.6 + - - +
104H GLY* 3.3 1.4 + - - -
105H ILE* 2.9 45.3 + - + +
152H VAL* 4.3 24.0 - - + -
156H LEU* 5.1 0.9 - - + -
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Residues in contact with GLN 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ARG* 4.0 25.2 + - - +
76H GLU* 5.3 5.0 + - - +
98H MET* 2.9 30.9 + - + +
99H GLY* 3.7 7.4 - - - +
100H GLU 3.2 0.4 - - - -
101H LEU* 1.3 74.5 - - - +
103H ARG* 1.3 63.7 + - + +
105H ILE* 3.1 24.0 + - - +
106H GLU* 2.9 43.3 + - + +
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Residues in contact with ARG 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H GLY 3.1 20.7 + - - +
100H GLU* 3.8 1.6 - - - +
102H GLN* 1.3 78.8 - - + +
104H GLY* 1.3 57.7 + - - +
106H GLU* 3.4 23.6 - - - +
107H ASN* 2.9 26.6 + - - +
150H PHE* 4.6 12.1 - - - -
153H MET* 3.1 46.1 - - - +
157H TRP* 5.2 0.8 - - - -
279H ARG* 5.9 3.4 - - - +
442H VAL* 3.8 39.7 - - - +
443H PRO 5.7 1.8 - - - -
444H VAL* 6.6 0.2 - - - +
445H ALA* 5.0 0.7 - - - +
449H PHE* 6.1 0.4 - - - -
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Residues in contact with GLY 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H GLU 3.1 12.8 + - - -
101H LEU 3.7 2.5 - - - -
103H ARG* 1.3 76.1 - - - +
105H ILE* 1.3 63.4 + - - +
107H ASN* 3.3 13.4 + - - +
108H VAL* 3.3 22.5 + - - +
153H MET* 3.9 7.1 - - - +
156H LEU* 3.6 31.2 - - - +
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Residues in contact with ILE 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ARG* 5.3 0.2 - - - +
72H LYS* 4.0 15.5 - - + -
75H LEU* 4.0 28.5 - - + -
76H GLU* 3.9 31.4 - - + +
79H ALA* 6.2 0.2 - - + -
98H MET* 6.2 0.4 - - + -
101H LEU* 2.9 36.4 + - + +
102H GLN* 3.5 30.5 - - - +
104H GLY* 1.3 73.6 - - - +
106H GLU* 1.3 58.4 + - - +
108H VAL* 2.9 10.7 + - - +
109H GLU* 2.9 42.5 + - - +
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Residues in contact with GLU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LEU* 4.1 15.7 - - + +
66F ARG* 3.5 24.0 + - - +
102H GLN* 2.9 25.9 + - + +
103H ARG* 3.4 27.9 - - - +
104H GLY 3.3 0.2 - - - -
105H ILE* 1.3 75.4 - - - +
107H ASN* 1.3 60.7 + - - +
109H GLU* 3.2 23.4 + - - +
110H TYR* 3.1 18.4 + - - +
444H VAL* 4.1 15.0 - - - +
445H ALA* 3.2 21.1 + - + +
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Residues in contact with ASN 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H ARG 2.9 18.7 + - - +
104H GLY* 3.3 11.8 + - - +
105H ILE 3.2 0.6 - - - -
106H GLU* 1.3 76.4 - - - +
108H VAL* 1.3 57.7 + - - +
110H TYR* 3.5 4.7 + - - +
111H ALA* 3.1 27.7 + - - +
156H LEU 3.3 25.2 - - - +
157H TRP* 3.3 22.5 + - - -
160H PRO* 4.5 3.8 - - + +
161H MET* 5.5 1.7 + - - +
445H ALA* 3.7 13.4 + - - +
463H TYR* 3.4 41.9 - - + +
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Residues in contact with VAL 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H MET* 3.1 43.6 - - + +
71H PHE* 3.8 25.4 - - + -
72H LYS* 3.9 19.5 - - + +
75H LEU* 4.0 7.6 - - + -
104H GLY 3.3 12.5 + - - +
105H ILE* 2.9 10.2 + - - +
107H ASN* 1.3 74.5 - - - +
109H GLU* 1.3 64.6 + - - +
111H ALA* 3.4 7.7 + - - +
112H CYS* 3.1 22.0 + - - -
156H LEU* 4.0 10.8 - - + -
160H PRO* 4.1 4.0 - - + -
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Residues in contact with GLU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LEU* 3.2 21.9 - - + +
66F ARG* 2.5 36.8 + - - +
69F PHE* 4.0 24.7 - - + -
112F CYS 5.4 2.0 - - - +
113F GLY* 5.6 3.6 - - - -
72H LYS* 3.0 37.6 + - + -
76H GLU* 5.0 0.2 - - - +
105H ILE* 2.9 18.9 + - - +
106H GLU* 3.2 20.3 + - - +
108H VAL* 1.3 73.2 - - - +
110H TYR* 1.3 66.3 + - - +
112H CYS* 3.1 20.3 + - - +
113H GLY 3.8 1.7 + - - -
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Residues in contact with TYR 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F GLY* 6.5 1.1 - - - -
116F GLU* 3.1 37.2 + - + -
106H GLU 3.1 9.3 + - - +
107H ASN* 3.8 8.7 - - - +
109H GLU* 1.3 78.5 - - - +
111H ALA* 1.3 57.5 + - - +
113H GLY* 3.0 21.7 + - - -
117H LEU* 3.1 38.6 - - + +
161H MET* 3.5 20.9 - - + -
445H ALA* 3.5 20.6 - - + +
446H TYR* 3.4 32.1 - + + -
464H GLY* 3.5 24.2 - - - -
465H PRO* 3.6 21.9 - - + +
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Residues in contact with ALA 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H MET* 4.4 6.7 - - + -
107H ASN 3.1 17.7 + - - +
108H VAL* 3.6 8.7 - - - +
109H GLU 3.2 0.2 - - - -
110H TYR* 1.3 73.4 - - - +
112H CYS* 1.3 59.7 + - - +
113H GLY 3.0 6.9 + - - -
114H ALA* 3.2 22.3 + - - +
117H LEU* 5.1 0.2 - - - -
160H PRO* 3.9 29.8 - - + +
161H MET* 4.3 12.8 - - + +
164H VAL* 3.5 18.6 - - + +
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Residues in contact with CYS 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F PHE* 4.0 12.8 - - + -
109F GLU* 5.4 2.6 - - - +
112F CYS* 5.8 0.4 - - + -
65H ALA* 3.4 25.3 - - - +
68H MET* 3.5 8.5 - - - +
69H PHE* 3.4 69.7 - - + -
72H LYS* 5.1 1.1 - - - -
108H VAL* 3.1 25.3 + - - -
109H GLU* 3.2 10.8 - - - +
111H ALA* 1.3 75.1 - - - +
113H GLY* 1.3 53.2 + - - +
114H ALA 3.4 1.4 + - - -
115H PRO* 4.2 2.9 - - - +
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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