Contacts of the strand formed by residues 34 - 38 (chain A) in PDB entry 1GO1
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 LEU 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LYS* 1.4 78.1 - - + +
35A ILE* 1.4 60.0 + - - +
36A ILE* 4.2 15.3 - - + -
58A ILE* 4.4 0.2 - - - -
59A PRO* 3.5 18.4 - - + +
61A TYR* 4.7 10.1 - - + -
85A VAL* 2.7 47.5 + - + +
93A ILE* 3.2 49.8 - - + +
94A LEU* 4.1 11.2 - - + +
96A LEU* 5.3 1.1 - - + -
97A GLY* 3.3 34.1 - - - +
98A GLY* 3.7 10.5 - - - -
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER* 4.3 15.0 - - - +
27A ALA* 4.0 28.5 - - + +
32A ALA* 4.1 13.7 - - + -
34A LEU* 1.4 75.5 - - - +
36A ILE* 1.4 60.3 + - - +
37A VAL* 4.5 7.4 - - + -
49A ILE* 3.5 24.9 - - + -
53A ALA* 4.0 10.1 - - + -
58A ILE* 3.7 28.5 - - + -
59A PRO 3.1 10.6 + - - +
60A VAL* 3.2 14.3 - - + +
61A TYR 3.0 22.1 + - - -
83A LEU 3.6 16.4 - - - +
84A ALA* 4.1 6.1 - - + -
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Residues in contact with ILE 36 (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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3A PHE* 3.7 30.7 - - + -
7A LEU* 4.2 2.0 - - + -
34A LEU* 4.1 9.8 + - + -
35A ILE* 1.4 72.7 - - - +
37A VAL* 1.4 61.6 + - - +
38A ALA 4.5 0.2 + - - -
61A TYR* 3.4 35.7 - - + +
63A PHE* 3.9 22.2 - - + -
70A LEU* 5.1 2.7 - - + +
82A ALA* 3.5 1.7 - - - -
83A LEU* 2.9 64.4 + - + +
85A VAL* 4.2 3.8 - - + -
93A ILE* 3.7 27.6 - - + -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 4.0 1.8 + - + -
36A ILE* 1.4 78.3 - - - +
38A ALA* 1.4 59.7 + - - +
46A LYS* 4.5 26.0 - - + +
49A ILE* 4.1 24.0 - - + -
50A GLU* 4.8 8.1 - - + -
60A VAL* 3.7 28.5 - - + -
61A TYR 3.0 11.6 + - - +
62A GLU* 3.5 16.5 - - + -
63A PHE* 2.8 33.0 + - - -
81A SER 3.9 4.0 - - - +
82A ALA* 3.9 15.9 - - + -
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Residues in contact with ALA 38 (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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36A ILE 4.5 0.2 + - - -
37A VAL* 1.4 70.1 - - - +
39A ARG* 1.4 64.7 + - - +
40A ASN 3.3 0.4 - - - +
41A ALA* 3.2 23.2 + - + +
46A LYS* 3.5 11.1 - - - +
63A PHE* 4.1 11.4 - - + -
66A THR 4.4 4.3 - - - -
67A SER* 4.2 18.2 - - - +
70A LEU* 4.0 18.2 - - + +
80A VAL 4.0 7.9 - - - +
81A SER 2.9 20.4 + - - +
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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