Contacts of the helix formed by residues 22 - 32 (chain A) in PDB entry 2GC5
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 HIS 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ASP* 1.3 100.3 + - + +
23A ARG* 1.3 62.0 + - - -
24A ARG 3.3 3.1 + - - -
25A ILE* 3.4 8.8 + - + +
26A LEU* 2.9 32.8 + - + +
122A GLU* 5.7 1.6 - - - -
149A ASP 3.2 25.5 + - - -
150A THR* 3.4 13.7 - - - -
151A ASP 2.7 31.6 + - - -
152A SER* 4.3 6.5 - - - -
154A ASN* 3.3 26.0 + - + -
155A VAL* 4.0 18.8 - - + +
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Residues in contact with ARG 23 (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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21A ASP* 3.0 27.5 + - - +
22A HIS* 1.3 77.1 - - - +
24A ARG* 1.3 64.2 + - + +
26A LEU* 3.8 29.8 - - - +
27A THR* 3.0 32.6 + - - +
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Residues in contact with ARG 24 (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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16A LEU* 3.5 27.7 + - - +
17A ALA* 2.6 34.9 + - - +
18A LYS* 4.5 6.5 + - - +
21A ASP 4.8 10.0 + - - +
22A HIS 3.3 0.4 - - - -
23A ARG* 1.3 78.4 - - + +
25A ILE* 1.3 62.8 + - - +
27A THR 3.2 8.5 + - - -
28A LEU 3.2 9.0 + - - -
116A PHE* 3.4 23.9 - - + -
117A ASN 3.4 24.5 - - - +
118A VAL* 3.9 4.1 - - + +
119A THR* 3.8 11.3 - - - +
122A GLU* 2.9 42.1 + - - +
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Residues in contact with ILE 25 (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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22A HIS* 3.4 18.1 + - + +
24A ARG* 1.3 79.5 - - - +
26A LEU* 1.3 55.0 + - - +
28A LEU* 3.1 6.5 + - + +
29A LEU* 2.8 46.7 + - + +
118A VAL* 4.8 0.4 - - - -
122A GLU* 3.5 44.7 + - + +
125A THR* 3.7 21.5 - - + -
126A ALA* 4.0 10.8 - - + +
152A SER* 3.7 36.8 - - - +
155A VAL* 4.0 14.6 - - + -
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Residues in contact with LEU 26 (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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21A ASP* 4.7 4.0 - - - +
22A HIS* 2.9 39.9 + - + +
23A ARG* 3.8 35.7 - - - +
25A ILE* 1.3 73.1 - - - +
27A THR* 1.3 60.6 + - - +
29A LEU* 3.8 4.5 - - + +
30A HIS* 2.9 30.3 + - - +
34A ASN* 4.6 2.0 - - - +
36A GLN* 4.1 17.7 - - - +
155A VAL* 3.8 28.0 - - + +
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Residues in contact with THR 27 (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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23A ARG* 3.0 19.9 + - - +
24A ARG 3.2 8.5 + - - -
26A LEU* 1.3 77.4 - - - +
28A LEU* 1.3 61.4 + - - +
30A HIS* 3.4 6.6 + - - +
31A ALA* 3.2 17.0 + - - +
109A LEU* 3.6 29.8 - - + +
113A GLN* 5.0 7.9 + - - +
116A PHE* 3.7 26.6 - - + -
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Residues in contact with LEU 28 (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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24A ARG 3.2 8.5 + - - +
25A ILE* 3.1 9.9 + - + +
27A THR* 1.3 77.3 - - - +
29A LEU* 1.3 64.7 + - - +
31A ALA* 3.1 7.6 + - - +
32A LEU* 3.1 21.8 + - + +
102A VAL* 3.9 29.6 - - + +
105A ALA* 4.1 19.5 - - + -
106A LEU* 4.3 11.7 - - + +
109A LEU* 3.9 15.5 - - + +
116A PHE* 4.3 0.4 - - + -
118A VAL* 4.3 30.3 - - + -
122A GLU 4.5 1.8 - - - +
123A PHE* 4.4 8.5 - - + -
126A ALA* 3.6 26.9 - - + -
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Residues in contact with LEU 29 (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 ILE* 2.8 40.7 + - + +
26A LEU* 4.0 5.8 - - + +
28A LEU* 1.3 69.5 - - - +
30A HIS* 1.3 64.4 + - - +
32A LEU* 2.9 12.8 + - + +
33A GLY 3.2 0.2 + - - -
34A ASN* 2.8 24.9 + - - -
35A PRO* 3.9 18.2 - - + -
36A GLN* 3.3 40.8 - - + +
126A ALA* 3.8 28.5 - - + +
129A TYR* 4.3 8.3 - - + -
155A VAL* 3.8 25.6 - - + -
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Residues in contact with HIS 30 (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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26A LEU 2.9 19.7 + - - +
27A THR* 3.5 7.9 + - - +
29A LEU* 1.3 75.7 - - - +
31A ALA* 1.3 65.0 + - - +
33A GLY* 3.1 14.7 + - - -
34A ASN* 3.4 27.9 + - - +
109A LEU* 5.9 3.0 - - - +
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Residues in contact with ALA 31 (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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27A THR 3.2 2.9 + - - +
28A LEU 3.1 12.4 + - - +
30A HIS* 1.3 81.4 + - - +
32A LEU* 1.3 59.1 + - - +
33A GLY 3.4 1.2 + - - -
101A PHE* 5.6 1.7 - - - -
105A ALA* 3.9 18.4 - - + +
108A ARG* 3.7 20.5 + - + +
109A LEU* 3.8 33.0 - - + -
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Residues in contact with LEU 32 (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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28A LEU* 3.1 15.9 + - + +
29A LEU* 2.9 12.4 + - + +
31A ALA* 1.3 76.1 - - - +
33A GLY* 1.3 60.4 + - - +
34A ASN 3.4 1.1 - - - -
35A PRO* 3.6 11.9 - - + +
101A PHE* 3.7 34.9 - - + -
102A VAL* 4.1 25.6 - - + -
105A ALA* 3.7 23.1 - - + -
126A ALA* 4.1 35.9 - - + +
130A TRP* 3.6 25.4 + - + -
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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