Contacts of the strand formed by residues 62 - 67 (chain A) in PDB entry 1SXG
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 THR 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LYS* 5.2 1.3 - - - +
60A THR 4.9 3.8 - - - +
61A THR* 1.3 74.5 - - - +
63A VAL* 1.3 66.7 + - - +
92A ASN* 3.3 26.5 + - - +
94A ILE* 3.9 12.3 - - - +
116A GLN* 3.2 24.0 - - + +
117A VAL* 3.5 4.8 - - - +
118A ASP* 2.7 53.3 + - - +
119A GLY 3.7 0.3 + - - -
115D LYS* 3.6 23.4 + - - +
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Residues in contact with VAL 63 (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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61A THR* 4.6 1.1 - - + -
62A THR* 1.3 80.0 + - - +
64A GLY* 1.3 60.5 + - - +
65A VAL* 4.2 3.8 - - + -
91A TYR* 3.8 30.3 - - + -
92A ASN 2.6 12.5 + - - +
93A ILE* 3.3 25.9 - - + +
94A ILE 3.0 23.0 + - - -
117A VAL* 4.4 1.1 - - - -
119A GLY 3.1 12.6 - - - +
121A ILE* 3.9 20.4 - - + -
302A MET* 4.1 7.0 - - + -
305A LEU* 4.3 6.1 - - + -
309A MET* 4.3 20.2 - - + -
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Residues in contact with GLY 64 (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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63A VAL* 1.3 73.7 - - - +
65A VAL* 1.3 62.7 + - - +
94A ILE 3.4 1.8 - - - -
112A MET* 3.4 29.8 - - - -
117A VAL* 4.0 3.4 - - - +
119A GLY 2.6 14.1 + - - -
120A ILE* 3.1 10.8 - - - +
121A ILE* 2.8 27.2 + - - +
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Residues in contact with VAL 65 (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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63A VAL* 4.2 6.1 - - + -
64A GLY* 1.3 79.2 - - - +
66A ILE* 1.3 67.8 + - - +
79A ALA* 4.5 12.8 - - + +
82A ILE* 4.4 17.7 - - + -
93A ILE* 4.0 29.6 - - + -
94A ILE 2.7 15.2 + - - +
95A LEU* 3.2 11.9 - - + +
96A SER 2.8 24.9 + - - -
112A MET* 4.5 1.3 - - - +
121A ILE* 3.3 15.0 - - + +
123A MET* 3.5 28.9 - - + -
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Residues in contact with ILE 66 (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 VAL* 1.3 75.6 - - - +
67A ILE* 1.3 64.4 + - - +
96A SER* 3.3 32.1 - - - +
98A SER* 5.6 2.2 - - - +
105A GLU 4.8 0.7 - - - +
108A LEU* 3.5 27.4 - - + -
109A LEU* 4.1 19.1 - - + -
112A MET* 4.9 11.4 - - + -
120A ILE* 4.2 12.8 - - + -
121A ILE 3.1 5.7 + - - +
122A PHE* 3.2 46.9 - - + -
123A MET* 3.0 34.2 + - - +
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Residues in contact with ILE 67 (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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66A ILE* 1.3 75.7 - - - +
68A PRO* 1.3 67.2 - - + +
69A ASP 3.5 24.5 - - - +
70A ILE* 4.5 11.4 - - + -
75A TYR* 4.1 8.1 - - + +
76A ALA* 4.6 14.4 - - + -
79A ALA* 3.8 16.2 - - + -
95A LEU* 3.8 16.4 - - + -
96A SER 3.1 11.4 + - - +
97A ASN* 3.5 6.5 - - + +
98A SER* 3.0 27.0 + - - -
123A MET* 3.4 32.1 - - + -
70D ILE* 4.8 12.6 - - + -
95D LEU* 6.1 1.1 - - + -
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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