Contacts of the helix formed by residues 95 - 105 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I GLN* 4.4 1.6 - - - +
91I PHE* 5.8 1.0 - - - +
92I SER* 3.4 34.5 + - - +
94I LYS* 1.3 75.6 - - + +
96I HIS* 1.3 63.8 + - - +
97I ARG 3.4 3.4 - - - -
98I LYS* 3.0 50.4 + - + +
99I ILE* 3.1 26.6 + - - +
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Residues in contact with HIS 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I SER* 5.9 2.4 - - - -
18I GLN* 3.1 42.2 + - + +
19I ILE* 4.1 13.1 + - + +
93I VAL 3.4 15.9 + - - -
94I LYS 3.0 14.1 + - - -
95I GLU* 1.3 70.5 - - - +
97I ARG* 1.3 65.3 + - - +
99I ILE* 3.2 4.2 + - + +
100I TYR* 3.0 26.9 + - - -
201I 35T 2.9 76.0 + + + +
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Residues in contact with ARG 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I GLN* 4.2 9.6 + - + +
19I ILE* 3.3 24.4 - - + +
20I PRO* 4.3 6.9 - - - +
23I GLU* 2.6 46.1 + - - -
95I GLU 3.4 0.6 - - - -
96I HIS* 1.3 78.2 - - - +
98I LYS* 1.3 65.3 + - + +
100I TYR* 3.3 8.6 + - - +
101I THR* 2.9 37.2 + - - +
104I TYR* 4.2 5.7 - - - -
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Residues in contact with LYS 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I PHE* 6.4 0.7 - - + -
95I GLU* 3.0 51.1 + - + +
96I HIS 3.3 0.4 - - - -
97I ARG* 1.3 80.2 - - + +
99I ILE* 1.3 62.2 + - - +
101I THR* 3.4 7.7 + - - -
102I MET* 3.2 36.2 + - + +
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Residues in contact with ILE 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I LEU* 3.9 9.9 - - + -
86I PHE* 5.1 2.0 - - + -
91I PHE* 4.1 14.1 - - + -
92I SER 3.6 22.0 - - - +
93I VAL* 4.0 9.9 - - - +
95I GLU 3.1 14.8 + - - +
96I HIS 3.4 6.7 - - - +
97I ARG 3.2 0.2 - - - -
98I LYS* 1.3 72.8 - - + +
100I TYR* 1.3 66.5 + - - +
102I MET* 3.2 12.0 + - + +
103I ILE* 3.1 31.8 + - + +
201I 35T 3.6 71.1 - - + -
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Residues in contact with TYR 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ILE* 3.7 30.1 - - + -
23I GLU* 3.2 24.7 - - + -
24I GLN* 3.7 22.9 + - - +
50I MET* 3.6 40.5 - - + +
51I LYS* 4.4 1.6 + - - -
54I LEU* 3.7 24.7 - - + +
96I HIS 3.0 20.3 + - - +
97I ARG* 3.8 12.3 - - - +
99I ILE* 1.3 76.4 - - - +
101I THR* 1.3 64.0 + - - +
103I ILE* 3.0 7.2 + - - +
104I TYR* 2.9 42.6 + + + -
201I 35T 3.7 24.9 - + + -
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Residues in contact with THR 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ARG* 2.9 27.4 + - - +
98I LYS* 3.5 12.6 - - - -
100I TYR* 1.3 78.4 - - - +
102I MET* 1.3 64.3 + - + +
104I TYR* 3.6 14.3 + - - +
105I ARG* 3.1 34.2 + - + +
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Residues in contact with MET 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I PHE* 3.7 48.7 - - + +
88I VAL* 4.2 21.1 - - - -
91I PHE* 3.9 28.0 - - + -
98I LYS* 3.2 26.0 + - + +
99I ILE* 3.2 18.1 + - + +
101I THR* 1.3 78.0 - - + +
103I ILE* 1.3 60.1 + - - +
105I ARG* 3.5 32.8 + - - +
106I ASN* 2.9 23.0 - - - +
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Residues in contact with ILE 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I LEU* 4.3 7.4 - - + -
50I MET* 3.8 12.1 - - + -
53I VAL* 4.1 14.6 - - + -
54I LEU* 3.6 37.2 - - + -
57I LEU* 3.6 20.9 - - + -
86I PHE* 3.8 20.4 - - + -
99I ILE* 3.1 19.9 + - + +
100I TYR* 3.0 7.9 + - - +
102I MET* 1.3 72.7 - - - +
104I TYR* 1.3 60.6 + - - +
105I ARG 3.0 2.2 - - - -
106I ASN* 2.7 28.0 + - - +
107I LEU* 3.6 24.3 - - + +
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Residues in contact with TYR 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLU* 2.8 46.8 + - - +
26I THR* 4.6 8.5 + - + -
28I VAL* 5.2 2.7 - - + -
50I MET* 3.6 25.5 - - + +
97I ARG* 4.2 5.4 - - - -
100I TYR* 2.9 44.4 + + + +
101I THR* 3.9 9.6 - - - +
102I MET 3.5 0.2 - - - -
103I ILE* 1.3 76.6 - - - +
105I ARG* 1.3 60.7 + - + +
106I ASN 3.1 1.1 + - - -
107I LEU* 3.4 34.6 - - + +
109I VAL* 5.7 5.6 - - + -
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Residues in contact with ARG 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I LYS* 4.3 13.0 + - - +
85I LEU 4.5 2.4 + - - -
86I PHE* 2.6 37.4 + - - +
88I VAL* 5.5 0.4 - - - +
101I THR* 3.1 25.6 - - + +
102I MET* 3.6 35.1 + - - +
103I ILE 2.9 1.4 + - - -
104I TYR* 1.3 78.0 - - + +
106I ASN* 1.3 65.9 + - - +
107I LEU 3.6 1.5 + - - -
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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