Contacts of the helix formed by residues 95 - 111 (chain C) in PDB entry 2Z3Q
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 95 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ALA 4.2 8.5 - - - +
24C THR* 4.7 6.8 - - + +
94C LYS* 1.3 78.0 - - - +
96C ILE* 1.3 65.3 + - - +
97C LYS* 3.4 17.5 + - - +
98C GLU* 3.1 34.6 + - - +
99C PHE* 3.0 20.4 + - - +
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 3.4 31.4 - - + -
21C ILE* 4.0 29.8 - - + +
22C ASP* 5.2 0.2 - - - -
23C ALA* 3.6 25.4 - - + +
25C LEU* 3.3 31.0 - - + -
50C ILE* 3.9 21.8 - - + -
95C ASN* 1.3 74.1 - - - +
97C LYS* 1.3 63.7 + - - +
99C PHE* 3.2 3.5 + - - +
100C LEU* 2.9 35.1 + - + +
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Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLU* 5.0 15.7 - - + +
17C GLN* 6.3 0.2 - - - +
95C ASN* 3.3 18.7 + - - +
96C ILE* 1.3 77.6 - - - +
98C GLU* 1.3 63.8 + - - +
100C LEU* 3.9 5.7 - - - +
101C GLN* 3.0 29.9 + - - +
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C THR* 4.5 1.3 - - - -
29C SER* 5.6 0.5 + - - -
94C LYS* 3.9 34.9 - - + +
95C ASN* 3.1 27.4 + - - +
97C LYS* 1.3 83.6 - - + +
99C PHE* 1.3 66.7 + - - +
101C GLN* 4.0 5.5 - - - +
102C SER* 2.9 29.8 + - - +
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Residues in contact with PHE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 3.6 24.2 - - + -
26C TYR 3.6 9.2 - - - -
27C THR* 3.4 28.8 + - - +
43C PHE* 3.4 52.3 - + - -
46C GLU* 3.5 26.9 - - + -
47C LEU* 3.9 8.5 - - + -
50C ILE* 3.9 23.6 - - + -
95C ASN 3.0 17.9 + - - +
96C ILE* 3.5 7.6 - - - +
98C GLU* 1.3 76.5 - - - +
100C LEU* 1.3 63.5 + - + +
102C SER 3.2 0.3 + - - -
103C PHE* 2.9 41.5 + + - +
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 3.9 29.2 - - + +
12C ILE* 4.7 8.3 - - + -
13C GLU* 3.8 39.0 - - + +
16C ILE* 4.0 9.2 - - + -
47C LEU* 4.4 4.7 - - + -
50C ILE* 4.3 9.6 - - + -
96C ILE* 2.9 41.5 + - + +
97C LYS* 4.0 3.4 - - - +
99C PHE* 1.3 85.6 - - + +
101C GLN* 1.3 65.5 + - - +
103C PHE* 3.5 3.7 - - + +
104C VAL* 2.9 31.3 + - + +
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Residues in contact with GLN 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LYS 3.0 18.7 + - - +
98C GLU* 4.0 7.0 - - - +
99C PHE 3.3 0.2 - - - -
100C LEU* 1.3 78.4 - - - +
102C SER* 1.3 62.7 + - - +
104C VAL* 3.4 14.7 + - - +
105C HIS* 3.2 55.0 + - + -
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C THR* 3.7 9.0 - - - +
28C GLU 4.0 5.5 - - - +
29C SER* 2.7 26.2 + - - -
43C PHE* 3.7 17.9 - - - -
98C GLU* 2.9 18.6 + - - +
99C PHE 3.6 3.6 - - - -
101C GLN* 1.3 74.0 - - - +
103C PHE* 1.3 65.9 + - - +
105C HIS* 3.4 11.7 + - - +
106C ILE* 3.0 24.6 + - - +
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Residues in contact with PHE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C VAL* 4.7 0.4 - - + -
9C LEU* 3.7 27.8 - - + -
40C MET* 3.9 11.7 - - - -
43C PHE* 3.5 53.3 - + + -
44C LEU* 3.8 23.8 - - + -
47C LEU* 4.0 15.5 - - + -
66C LEU* 4.0 11.7 - - + -
99C PHE* 2.9 29.2 + + - +
100C LEU* 3.5 8.3 - - + +
102C SER* 1.3 73.9 - - - +
104C VAL* 1.3 67.0 + - - +
106C ILE* 3.2 8.1 - - + +
107C VAL* 3.0 42.1 + - + +
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.8 17.2 - - + +
9C LEU* 3.6 30.9 - - + +
10C LYS* 5.6 4.3 - - + +
100C LEU* 2.9 21.4 + - + +
101C GLN* 3.6 19.7 - - - +
103C PHE* 1.3 78.6 - - - +
105C HIS* 1.3 63.8 + - + +
107C VAL* 3.2 4.2 + - - +
108C GLN* 3.0 44.9 + - + +
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Residues in contact with HIS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C GLN* 3.2 46.5 + - + -
102C SER* 3.6 13.5 + - - +
103C PHE 3.3 0.2 - - - -
104C VAL* 1.3 78.4 - - + +
106C ILE* 1.3 61.5 + - - +
108C GLN* 3.4 21.5 + - - +
109C MET* 3.4 24.6 + - + +
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Residues in contact with ILE 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLU 5.6 0.2 - - - +
31C VAL* 4.3 17.0 - - + +
36C LYS 3.7 24.0 - - - +
39C ALA* 3.8 14.4 - - + -
40C MET* 3.7 26.0 - - + +
43C PHE* 3.7 22.2 - - + -
102C SER 3.0 16.5 + - - +
103C PHE* 3.2 17.0 - - + +
105C HIS* 1.3 73.2 - - - +
107C VAL* 1.3 68.6 + - - +
109C MET* 3.0 35.9 + - - +
110C PHE* 3.3 19.7 + - + -
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C TRP* 3.4 44.9 - - + +
5C VAL* 3.8 15.3 - - + -
6C ILE* 3.9 13.5 - - + -
9C LEU* 4.4 1.8 - - + -
40C MET* 3.8 16.8 - - + -
103C PHE* 3.0 43.3 + - + +
104C VAL* 3.7 4.0 - - - +
106C ILE* 1.3 74.6 - - - +
108C GLN* 1.3 56.9 + - - +
110C PHE* 2.8 20.7 + - - +
111C ILE* 3.4 9.5 + - - +
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.7 22.9 - - + +
104C VAL* 3.0 32.8 + - + +
105C HIS* 3.7 25.3 - - - +
106C ILE 3.3 0.2 - - - -
107C VAL* 1.3 74.2 - - - +
109C MET* 1.3 59.8 + - - +
110C PHE 3.4 0.3 + - - -
111C ILE* 3.4 27.9 + - + +
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Residues in contact with MET 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 4.1 37.7 - - + -
36C LYS* 4.4 28.6 - - + +
105C HIS* 3.4 14.3 + - + +
106C ILE* 3.0 22.2 + - - +
107C VAL 3.0 0.2 - - - -
108C GLN* 1.3 80.6 - - - +
110C PHE* 1.3 58.5 + - - +
111C ILE 4.4 3.5 - - - +
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Residues in contact with PHE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C TRP* 3.4 44.1 + + + +
36C LYS* 3.4 56.5 - - + -
37C VAL* 4.0 15.5 - - + -
40C MET* 3.3 31.4 - - + -
74C LEU* 3.9 17.7 - - + -
106C ILE* 3.3 18.3 + - + -
107C VAL 2.8 10.6 + - - +
109C MET* 1.3 77.2 - - - +
111C ILE* 1.3 60.9 + - - +
112C ASN* 3.5 13.6 + - - +
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Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C SER* 4.5 9.2 - - - +
2C TRP* 3.5 24.2 - - + -
3C VAL* 3.9 27.4 - - + +
6C ILE* 3.8 28.0 - - + -
107C VAL 3.6 6.5 - - - +
108C GLN* 3.4 21.1 + - + +
109C MET 4.4 3.6 - - - +
110C PHE* 1.3 79.7 - - - +
112C ASN* 1.3 74.1 + - - +
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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
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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