Contacts of the strand formed by residues 41 - 45 (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 TYR 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PRO 3.1 15.1 + - - -
36A GLN* 3.4 22.5 - - - -
37A GLN 5.2 0.4 - - - -
38A GLN 2.7 30.6 + - - -
39A GLY 3.8 8.1 - - - -
40A ARG* 1.3 81.6 - - - +
42A ILE* 1.3 66.3 + - - +
129A TYR* 3.6 24.9 + + - -
132A PHE* 5.5 2.5 - + + -
133A ARG* 3.9 9.1 - - - +
139A VAL* 4.1 2.0 - - - -
140A ALA* 3.2 26.2 - - + +
142A ILE* 3.9 12.3 - - + -
156A ILE* 3.7 32.5 - - + -
157A THR 4.3 10.3 + - - -
158A PRO* 3.3 8.3 - - + +
159A VAL* 2.8 35.6 + - - +
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Residues in contact with ILE 42 (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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41A TYR* 1.3 79.7 - - - +
43A HIS* 1.3 57.7 + - - +
44A VAL* 4.0 16.1 + - + -
57A ILE* 3.8 16.8 - - + -
61A LEU* 3.6 31.2 - - + -
139A VAL* 4.1 7.2 - - + -
140A ALA 2.9 9.5 + - - +
141A VAL* 3.4 9.8 - - + +
142A ILE* 2.8 32.3 + - - +
160A VAL* 3.6 16.6 - - + +
162A VAL* 4.3 2.7 - - + -
271A THR* 3.8 24.0 - - + -
275A TYR* 3.8 29.6 - - + -
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Residues in contact with HIS 43 (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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42A ILE* 1.3 71.9 - - - +
44A VAL* 1.3 61.0 + - - +
142A ILE* 3.4 25.4 - - + -
144A VAL* 3.5 11.6 - - + +
153A THR* 3.0 31.4 + - - -
154A ASN* 3.7 25.8 + - + -
156A ILE* 3.7 15.8 - - + +
158A PRO* 3.9 24.7 - - + +
160A VAL 3.2 7.7 + - - +
161A SER* 3.5 1.6 - - - +
162A VAL* 2.8 26.7 + - - +
188A ILE* 3.4 38.8 + - + +
190A LYS* 5.0 1.4 + - - -
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Residues in contact with VAL 44 (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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42A ILE* 4.2 13.0 - - + -
43A HIS* 1.3 80.2 - - - +
45A THR* 1.3 65.0 + - - +
50A LYS* 3.6 34.2 - - + +
53A ALA* 4.5 2.7 - - + -
54A ALA* 4.2 13.2 - - + +
57A ILE* 4.3 6.1 - - + -
141A VAL* 4.1 26.2 - - + -
142A ILE 2.8 13.5 + - - +
143A GLU* 3.4 3.9 - - - -
144A VAL* 2.8 30.8 + - - +
162A VAL* 3.6 24.7 - - + -
164A THR* 4.6 0.2 - - + -
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Residues in contact with THR 45 (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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44A VAL* 1.3 76.4 - - - +
46A GLY* 1.3 62.5 + - - +
50A LYS* 4.0 10.3 - - - -
144A VAL* 3.5 20.0 - - - +
147A GLY 2.5 26.6 + - - +
162A VAL 2.8 14.7 + - - +
163A LEU* 3.3 20.9 - - + -
164A THR* 3.0 27.4 + - - +
185A KCX 3.6 15.9 + - + +
188A ILE* 3.5 23.1 - - + +
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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