Contacts of the strand formed by residues 72 - 77 (chain A) in PDB entry 4GQS
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 GLU 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LEU 4.0 0.2 - - - +
68A TYR* 3.7 3.6 - - - -
69A PHE* 2.8 37.7 + - - +
70A GLY 3.3 0.2 - - - -
71A LEU* 1.3 80.8 - - - +
73A ARG* 1.3 74.4 + - - +
74A MET* 4.0 17.0 + - + +
99A HIS* 2.6 47.9 + - + +
217A ASN 4.7 2.9 - - - +
218A ASN* 4.2 22.0 - - - +
386A THR* 2.9 25.8 + - - -
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Residues in contact with ARG 73 (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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29A LEU* 3.1 38.5 - - - +
66A THR* 4.0 14.3 - - + +
67A LEU 3.5 5.6 - - - -
68A TYR* 3.1 43.0 + - + -
71A LEU 3.9 3.0 + - - +
72A GLU* 1.3 87.2 + - - +
74A MET* 1.3 65.0 + - - +
382A PRO* 4.4 16.0 - - - +
385A THR* 4.2 21.4 + - + +
386A THR* 3.8 11.4 + - - -
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Residues in contact with MET 74 (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 THR* 3.3 4.9 - - - +
67A LEU* 2.7 53.8 + - + +
69A PHE* 3.4 30.5 - - + -
72A GLU* 4.1 26.5 - - + +
73A ARG* 1.3 74.7 - - - +
75A VAL* 1.3 65.5 + - - +
76A VAL* 4.1 1.7 + - + -
218A ASN* 4.5 12.6 - - - +
385A THR* 4.7 0.4 - - - -
386A THR* 3.3 34.5 - - + +
388A LEU* 3.9 29.4 - - + -
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Residues in contact with VAL 75 (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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29A LEU* 5.1 3.1 - - + -
30A PRO* 4.3 9.4 - - + -
64A VAL* 3.9 28.0 - - + -
65A PHE 3.4 6.5 - - - +
66A THR* 4.3 16.4 - - + +
74A MET* 1.3 76.1 - - - +
76A VAL* 1.3 67.3 + - - +
77A LEU* 4.5 5.4 - - + -
381A ILE* 4.4 19.3 - - + -
385A THR* 4.1 19.5 - - + -
386A THR 3.0 6.3 + - - -
387A ILE* 3.4 24.0 - - + +
388A LEU 2.9 22.1 + - - -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.8 28.9 - - + -
63A PRO 3.2 12.8 - - - +
64A VAL* 3.4 2.6 - - - -
65A PHE* 2.8 65.8 + - + +
67A LEU* 3.8 20.2 - - + -
74A MET* 4.9 2.2 - - + +
75A VAL* 1.3 74.4 - - - +
77A LEU* 1.3 70.6 + - - +
78A HIS* 3.8 4.2 + - + +
388A LEU* 3.3 21.1 - - + +
390A SER* 5.0 3.4 - - - -
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Residues in contact with LEU 77 (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 PRO 3.4 1.1 - - - -
64A VAL* 4.0 18.2 - - + -
75A VAL* 4.5 6.1 - - + -
76A VAL* 1.3 77.2 - - - +
78A HIS* 1.3 59.0 + - - +
82A VAL* 4.0 12.8 - - + +
83A VAL* 3.8 13.3 - - + +
86A ALA* 3.5 31.0 - - + -
87A LEU* 5.9 0.9 - - + -
94A PHE* 4.2 5.2 - - + -
376A PHE* 3.8 26.7 - - + -
381A ILE* 5.7 1.3 - - + -
387A ILE* 3.6 29.6 - - + -
388A LEU 2.9 11.9 + - - +
389A THR* 3.8 13.5 - - + -
390A SER 3.1 23.8 + - - -
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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