Contacts of the helix formed by residues 29 - 33 (chain A) in PDB entry 3GSB
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 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.2 16.3 + - - +
28A SER* 1.3 82.4 - - - +
30A PRO* 1.4 76.3 - - - +
31A VAL* 4.0 2.9 - - - +
32A ARG* 3.1 20.9 + - - +
500A GAB 3.0 47.4 + - - -
118B ARG* 4.4 0.9 - - - +
296B PRO* 4.8 0.2 - - - -
303B ALA* 3.5 5.1 - - - +
304B GLY 3.5 10.7 + - - -
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Residues in contact with PRO 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.2 0.6 - - - -
29A SER* 1.4 88.5 - - - +
31A VAL* 1.3 59.5 + - - +
32A ARG 3.3 0.2 - - - -
33A ALA* 3.2 21.5 - - - +
164A GLY* 5.5 0.4 - - - -
168A LEU* 3.6 25.6 - - + +
118B ARG* 4.2 0.9 - - - +
295B ALA* 3.4 30.3 - - + +
296B PRO* 3.8 13.0 - - + -
301B TYR* 3.6 24.7 - - + +
302B GLN 3.2 26.2 - - - +
303B ALA* 3.7 7.2 - - + -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 3.1 1.1 + - - +
30A PRO* 1.3 72.5 - - - +
32A ARG* 1.3 60.6 + - + +
33A ALA 3.0 11.5 + - - +
67A TRP* 3.6 24.0 - - + -
163A SER* 4.2 2.0 - - - +
164A GLY* 4.1 15.9 - - - +
167A THR* 6.0 4.7 - - - +
402A PRO* 3.5 23.4 - - - +
406A GLU* 4.7 5.8 - - + +
500A GAB 3.3 57.4 - - + +
301B TYR* 3.9 19.5 - - - +
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Residues in contact with ARG 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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27A VAL* 4.0 13.9 - - + +
28A SER* 3.9 7.9 - - - +
29A SER* 3.1 24.7 + - - +
31A VAL* 1.3 76.2 - - + +
33A ALA* 1.3 58.8 + - - +
34A PHE* 3.7 7.6 - - - -
41A PRO* 3.4 24.6 - - - +
67A TRP* 5.4 1.3 - - - -
402A PRO* 5.3 1.3 - - - -
500A GAB 2.7 27.8 + - - +
94B GLY* 3.4 31.0 + - - +
95B ALA* 3.9 19.4 + - - +
96B PRO* 4.3 12.8 - - + +
100B GLU* 3.6 18.8 + - - -
304B GLY 3.7 2.2 + - - -
305B THR 2.8 29.5 + - - -
306B LEU 4.5 0.2 - - - -
307B SER 2.9 26.9 + - - -
308B GLY* 4.7 2.2 + - - -
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Residues in contact with ALA 33 (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 PHE* 5.8 2.7 - - + -
25A GLY 5.4 1.6 - - - +
27A VAL* 4.2 8.3 - - + +
29A SER 4.2 0.6 + - - -
30A PRO 3.2 17.0 + - - +
31A VAL 3.0 8.5 - - - +
32A ARG* 1.3 77.6 - - - +
34A PHE* 1.3 61.5 + - - +
35A LYS* 3.0 25.6 + - + +
36A SER* 4.7 1.7 + - - -
41A PRO* 4.3 4.7 - - - -
167A THR* 5.7 3.8 - - - +
168A LEU* 5.4 1.0 - - + +
402A PRO* 4.6 6.2 - - - +
296B PRO* 3.8 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