Contacts of the helix formed by residues 95 - 105 (chain K) in PDB entry 4QOC
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 GLU 95 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92K SER* 3.2 30.4 + - - +
94K LYS* 1.3 77.2 - - + +
96K HIS* 1.3 59.7 + - - +
97K ARG 3.5 2.2 - - - -
98K LYS* 3.1 39.7 + - + +
99K ILE* 3.1 29.4 + - - +
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Residues in contact with HIS 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K ILE* 3.3 26.4 - - + +
93K VAL 3.2 17.0 + - - -
94K LYS* 3.3 13.7 + - - -
95K GLU* 1.3 66.3 - - - +
97K ARG* 1.3 65.9 + - - +
98K LYS 3.1 1.8 - - - -
99K ILE* 3.1 4.3 + - + +
100K TYR* 3.0 30.1 + - + -
201K 35T 2.6 74.1 + + + -
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Residues in contact with ARG 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K GLN* 3.5 45.8 - - - +
19K ILE* 4.0 19.7 - - + +
95K GLU 3.5 0.6 - - - -
96K HIS* 1.3 76.9 - - - +
98K LYS* 1.3 64.1 + - + +
100K TYR* 3.3 10.5 + - + +
101K THR* 3.1 27.0 + - + +
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Residues in contact with LYS 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K PHE* 6.5 0.4 - - + -
95K GLU* 3.1 42.4 + - + +
96K HIS 3.1 0.4 - - - -
97K ARG* 1.3 78.8 - - + +
99K ILE* 1.3 62.9 + - + +
101K THR* 2.5 28.1 + - - +
102K MET* 3.2 16.7 + - + +
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Residues in contact with ILE 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K PHE* 5.0 0.4 - - + -
91K PHE* 4.2 5.4 - - + -
92K SER 3.6 21.1 - - - +
93K VAL* 4.0 14.8 - - - +
95K GLU 3.1 14.3 + - - +
96K HIS* 3.1 6.9 + - - +
98K LYS* 1.3 77.7 - - + +
100K TYR* 1.3 62.6 + - - +
102K MET* 3.0 24.4 + - + +
103K ILE* 2.9 40.3 + - + +
201K 35T 3.6 59.0 - - + -
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Residues in contact with TYR 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K ILE* 4.0 31.1 - - + +
23K GLU* 3.6 23.8 - - + +
24K GLN* 3.6 17.7 + - - +
50K MET* 3.7 33.7 - - + -
54K LEU* 3.4 26.2 - - + +
96K HIS* 3.0 25.0 + - - -
97K ARG* 3.7 10.8 - - + +
98K LYS 3.3 0.2 - - - -
99K ILE* 1.3 76.9 - - - +
101K THR* 1.3 58.0 + - + +
103K ILE* 3.2 8.4 + - + +
104K TYR* 2.8 46.4 + - + -
201K 35T 3.6 22.8 - + + -
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Residues in contact with THR 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K ARG* 3.1 16.5 + - + +
98K LYS* 2.5 25.4 + - + +
99K ILE 3.1 0.2 - - - -
100K TYR* 1.3 77.7 - - + +
102K MET* 1.3 64.1 + - - +
104K TYR* 3.7 8.8 + - + +
105K ARG* 3.4 21.5 + - - +
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Residues in contact with MET 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K PHE* 3.5 61.4 - - + +
88K VAL* 3.8 21.5 - - + -
91K PHE* 3.7 29.4 - - + -
98K LYS* 3.4 11.2 - - + +
99K ILE* 3.0 27.7 + - + +
101K THR* 1.3 78.1 - - - +
103K ILE* 1.3 62.4 + - - +
105K ARG* 3.2 20.4 - - - +
106K ASN* 3.0 20.8 - - - +
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Residues in contact with ILE 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K LEU* 5.3 3.1 - - + -
50K MET* 4.1 15.3 - - + -
53K VAL* 4.4 10.1 - - + -
54K LEU* 3.6 31.9 - - + -
57K LEU* 3.8 24.7 - - + -
86K PHE* 4.0 11.7 - - + -
99K ILE* 2.9 30.5 + - + +
100K TYR* 3.7 11.4 - - + +
102K MET* 1.3 72.9 - - - +
104K TYR* 1.3 60.1 + - - +
105K ARG 3.0 2.2 - - - -
106K ASN* 2.9 24.1 + - - +
107K LEU* 3.4 30.7 - - + +
201K 35T 4.6 1.8 - - + -
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Residues in contact with TYR 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K GLU* 2.5 39.0 + - - -
26K THR* 4.8 3.5 + - + +
31K LYS* 4.8 1.6 + - - -
50K MET* 4.2 15.4 - - + +
100K TYR* 2.8 37.7 + - + +
101K THR* 4.1 8.7 - - + +
102K MET 3.4 0.4 - - - -
103K ILE* 1.3 76.1 - - + +
105K ARG* 1.3 60.9 + - - +
106K ASN 3.1 0.8 + - - -
107K LEU* 3.4 34.1 - - + +
109K VAL* 3.9 24.2 - - + +
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Residues in contact with ARG 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K LYS* 2.9 25.6 + - - +
84K ASP 5.3 2.2 + - - -
85K LEU 3.8 9.7 + - - +
86K PHE 3.6 19.6 + - - -
87K GLY* 3.6 23.4 + - - -
101K THR 3.4 12.3 + - - +
102K MET* 3.2 21.1 - - - +
103K ILE 3.0 0.6 - - - -
104K TYR* 1.3 77.9 - - - +
106K ASN* 1.3 64.8 + - - +
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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