Contacts of the helix formed by residues 91 - 104 (chain A) in PDB entry 4GEK
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 SER 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PHE* 2.6 36.8 + - - -
89A ASP* 3.0 14.0 + - - -
90A ASN* 1.3 79.3 + - - +
92A PRO* 1.3 68.2 - - - +
93A ALA 3.4 1.9 + - - -
94A MET* 3.1 16.5 + - - +
95A ILE* 3.0 23.7 + - - +
115A GLU* 5.0 0.4 - - - -
302A GEK 3.7 10.1 - - - -
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Residues in contact with PRO 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE 5.5 0.7 - - - +
90A ASN 3.4 8.9 - - - +
91A SER* 1.3 84.9 - - - +
93A ALA* 1.3 57.5 + - - +
95A ILE* 3.7 7.4 - - + +
96A GLU* 2.9 30.8 + - - +
115A GLU* 3.5 27.6 - - - +
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE 3.7 6.7 - - - +
21A ASP* 3.5 35.9 - - - +
22A GLU* 3.6 12.1 - - + +
25A ALA* 3.9 5.2 - - + +
91A SER* 3.2 1.4 + - - -
92A PRO* 1.3 76.3 - - - +
94A MET* 1.3 66.9 + - - +
96A GLU* 3.6 9.3 + - - +
97A ARG* 3.3 22.9 + - - +
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Residues in contact with MET 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.5 32.1 - - + +
24A VAL* 4.2 7.6 - - + -
25A ALA* 4.3 8.7 - - + +
28A PHE* 3.6 31.9 - - + -
66A SER* 3.6 20.7 - - - +
67A LEU* 3.6 26.2 - - - +
89A ASP* 3.9 8.7 - - - +
91A SER* 3.1 29.0 + - - +
93A ALA* 1.3 77.8 - - - +
95A ILE* 1.3 58.5 + - - +
97A ARG* 3.3 1.6 + - - -
98A CYS* 2.7 30.8 + - - +
302A GEK 3.6 17.9 - - - +
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A CYS* 4.4 6.1 - - - -
89A ASP* 3.5 31.4 - - + +
91A SER 3.0 20.1 + - - +
92A PRO* 3.7 7.4 - - + +
94A MET* 1.3 77.8 - - - +
96A GLU* 1.3 64.8 + - - +
98A CYS* 3.5 2.9 - - - +
99A ARG* 2.9 26.0 + - + +
113A VAL* 3.6 27.9 - - + +
114A ILE 3.4 24.0 - - - +
115A GLU* 3.9 21.8 - - + +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PRO 2.9 17.1 + - - +
93A ALA* 3.9 7.8 - - - +
95A ILE* 1.3 80.3 - - - +
97A ARG* 1.3 63.0 + - - +
99A ARG* 3.5 4.6 + - - +
100A ARG* 3.3 52.2 + - - +
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 2.8 42.3 + - + -
26A GLU* 3.1 24.4 + - - +
29A PRO* 3.8 13.1 - - - +
67A LEU* 3.5 33.0 - - + +
93A ALA 3.3 12.7 + - - +
96A GLU* 1.3 76.4 - - - +
98A CYS* 1.3 59.7 + - - +
100A ARG* 3.3 13.9 + - + +
101A HIS* 2.8 45.0 + - + +
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Residues in contact with CYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A CYS* 4.0 14.8 - - - -
66A SER 3.2 18.8 - - - +
67A LEU* 3.6 24.8 - - - +
68A GLY* 3.8 4.0 - - - -
87A ALA* 4.9 0.2 - - - -
94A MET 2.7 22.0 + - - +
95A ILE* 3.5 8.5 - - - +
97A ARG* 1.3 72.6 - - - +
99A ARG* 1.4 57.9 + - - +
101A HIS* 3.2 0.9 + - - +
102A ILE* 2.8 51.1 + - - +
113A VAL* 4.1 11.0 - - + -
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ARG* 5.7 1.0 - - - +
95A ILE* 2.9 19.1 + - + +
96A GLU* 3.9 5.4 - - - +
98A CYS* 1.4 75.1 - - - +
100A ARG* 1.3 63.4 + - - +
102A ILE* 3.3 30.3 + - - +
103A ASP* 2.5 51.2 + - - +
111A VAL* 2.8 30.1 + - - +
113A VAL* 3.8 33.2 - - + +
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Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.3 48.4 + - - +
97A ARG* 3.3 14.3 + - + +
98A CYS 3.2 0.4 - - - -
99A ARG* 1.3 81.7 - - - +
101A HIS* 1.3 61.6 + - - +
103A ASP* 3.3 10.0 + - + +
104A ALA* 3.3 19.8 + - - +
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Residues in contact with HIS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.4 31.0 - - + +
72A LEU* 3.5 20.0 - - + +
97A ARG* 2.8 36.7 + - + +
98A CYS 3.6 3.6 - - - +
100A ARG* 1.3 77.4 - - - +
102A ILE* 1.4 61.6 + - - +
104A ALA* 3.1 13.4 + - - +
105A TYR* 3.1 41.6 + + - -
301A SO4 2.6 36.1 + - - -
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU 4.6 3.1 - - - +
68A GLY* 4.4 1.6 - - - -
71A THR* 3.7 27.4 - - + +
72A LEU* 4.0 26.2 - - + -
75A ARG* 4.0 15.9 + - - +
87A ALA* 4.8 0.7 - - + -
98A CYS* 2.8 44.1 + - - +
99A ARG* 3.3 22.0 - - - +
101A HIS* 1.4 70.2 - - - +
103A ASP* 1.3 61.9 + - - +
104A ALA 3.0 1.6 + - - -
105A TYR* 3.1 21.1 + - - +
111A VAL* 3.9 31.2 - - + -
113A VAL* 4.1 3.8 - - + -
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Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG* 2.5 65.4 + - - +
100A ARG* 3.6 10.1 - - + +
101A HIS 3.1 0.4 - - - -
102A ILE* 1.3 76.6 - - - +
104A ALA* 1.3 60.4 + - - +
105A TYR 3.2 4.1 + - - +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG 3.3 9.9 + - - +
101A HIS* 3.1 16.7 + - - +
102A ILE 3.0 1.4 + - - -
103A ASP* 1.3 76.8 - - - +
105A TYR* 1.3 77.0 + - + +
106A LYS* 4.3 1.6 + - - +
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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