Contacts of the strand formed by residues 610 - 616 (chain A) in PDB entry 3WSZ
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 TRP 610 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A SER* 3.8 2.6 - - - -
98A LEU* 3.1 31.6 + - + +
100A ASP* 3.1 46.3 + - + +
102A HIS 2.5 27.7 + - - -
103A ASN 3.6 19.7 - - - -
104A GLN 4.6 2.2 + - - -
105A MET* 3.4 54.0 - - + +
584A TYR* 4.3 31.2 - + + -
600A PHE* 4.2 24.9 - + + -
601A GLY 3.8 13.2 - - - -
602A SER* 4.9 0.9 - - - +
608A HIS* 3.6 12.6 + + - -
609A SER* 1.3 76.5 + - - +
611A LEU* 1.3 61.5 + - - +
612A ILE* 5.4 0.9 - - + -
9C ALA* 4.8 3.1 - - + -
11C ALA 4.0 11.9 - - - -
12C ALA* 4.8 2.2 - - + -
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Residues in contact with LEU 611 (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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95A GLN* 5.5 3.1 - - + +
96A VAL 3.5 11.4 - - - +
97A SER* 3.1 29.8 - - - +
581A VAL* 4.1 28.3 - - + -
599A ILE 3.6 3.3 - - - +
600A PHE* 3.6 2.6 - - - -
601A GLY* 2.7 38.3 + - - +
602A SER* 4.2 1.6 - - - -
603A ASN* 4.1 19.1 - - + +
609A SER 4.1 4.7 - - - +
610A TRP* 1.3 77.8 - - - +
612A ILE* 1.3 64.9 + - - +
613A LEU* 4.0 28.0 - - + +
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Residues in contact with ILE 612 (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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94A GLY 3.6 3.5 - - - +
96A VAL* 2.8 43.2 + - + +
98A LEU* 4.4 23.8 - - + -
105A MET* 4.5 11.9 - - + -
107A VAL* 5.5 0.9 - - + -
119A ALA* 5.4 4.0 - - + -
142A GLY* 4.8 2.2 - - - +
145A PHE* 4.2 33.7 - - + -
598A THR* 3.7 26.7 - - + -
599A ILE 3.7 2.0 - - - +
600A PHE* 3.8 26.2 - - + -
610A TRP* 5.8 0.2 - - + -
611A LEU* 1.3 80.2 - - - +
613A LEU* 1.3 63.0 + - - +
614A GLN* 3.9 4.9 + - - +
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Residues in contact with LEU 613 (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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92A VAL* 4.6 5.8 - - + -
94A GLY 3.4 0.9 - - - +
95A GLN* 3.6 43.3 - - + +
576A PHE* 3.6 39.5 - - + +
577A SER* 4.8 8.3 - - - -
581A VAL* 4.9 3.6 - - + -
597A PHE 3.8 0.5 - - - +
598A THR* 3.4 4.7 - - - +
599A ILE* 2.8 57.6 + - + +
611A LEU* 4.5 28.5 - - + +
612A ILE* 1.3 73.6 - - - +
614A GLN* 1.3 63.0 + - - +
615A VAL* 3.8 5.4 - - + -
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Residues in contact with GLN 614 (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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92A VAL* 3.3 2.7 - - - -
93A TYR* 2.6 47.2 + - + -
94A GLY 2.7 24.4 + - - +
109A TRP* 5.0 2.0 - - - +
117A ILE* 4.3 9.3 - - - +
141A TYR* 3.1 38.3 + - - +
142A GLY* 4.0 15.9 - - - +
596A VAL* 3.4 27.6 - - + +
598A THR* 2.8 36.2 + - - +
612A ILE* 4.6 3.2 - - - +
613A LEU* 1.3 71.5 - - - +
615A VAL* 1.3 55.9 + - - +
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Residues in contact with VAL 615 (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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90A ILE* 3.4 26.5 - - + -
91A LYS 3.6 2.9 - - - -
92A VAL* 4.3 11.9 - - + +
93A TYR* 5.1 0.2 - - - -
561A LEU* 3.8 16.8 - - + -
574A PHE* 4.6 0.4 - - + -
576A PHE* 4.2 16.2 - - + -
595A THR 4.0 0.7 - - - +
596A VAL* 3.3 7.0 - - - +
597A PHE* 2.9 47.7 + - + +
599A ILE* 3.9 28.9 - - + -
613A LEU* 4.9 2.5 - - + -
614A GLN* 1.3 76.4 - - - +
616A ASN* 1.3 62.9 + - - +
617A ALA* 4.8 4.9 - - + +
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Residues in contact with ASN 616 (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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89A PRO 4.3 0.9 - - - +
90A ILE* 3.5 2.9 - - - -
91A LYS* 2.6 46.4 + - + +
93A TYR* 4.2 16.6 - - + +
595A THR* 3.9 5.0 + - - +
596A VAL* 4.4 7.6 - - + +
615A VAL* 1.3 72.9 - - - +
617A ALA* 1.3 60.8 + - - +
618A THR* 3.2 14.6 + - - -
619A ASP 5.1 0.3 + - - -
803A NAG 1.5 70.4 + - - +
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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