Contacts of the strand formed by residues 497 - 503 (chain A) in PDB entry 2CAS
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 GLN 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LEU* 3.8 15.5 - - + +
113A ASP* 4.8 3.8 - - - +
176A ALA 3.7 0.9 - - - +
177A LEU* 3.5 3.0 - - - -
178A ASP* 2.9 32.9 + - - +
181A ASN* 4.0 13.4 - - - +
183A MET 4.6 3.0 + - - -
184A PRO 3.0 28.5 + - - -
185A PHE* 3.2 30.1 - - + +
186A THR* 3.2 29.8 + - - +
187A PRO* 5.2 0.2 - - - +
208A TRP* 4.6 0.6 - - - +
496A GLY* 1.4 75.8 - - - -
498A LEU* 1.3 59.7 + - - +
499A PHE* 3.6 28.4 - - + -
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Residues in contact with LEU 498 (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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111A LEU* 3.6 7.8 - - - +
112A VAL* 2.9 59.5 + - + +
143A GLN* 3.8 37.2 - - + +
145A ILE* 3.8 23.3 - - + -
175A VAL* 3.8 27.8 - - + -
176A ALA 3.6 2.0 - - - +
177A LEU* 4.0 16.8 - - + -
261A PHE* 3.9 16.8 - - + -
263A THR* 4.6 1.1 - - - +
496A GLY 3.9 0.4 + - - -
497A GLN* 1.3 72.9 - - - +
499A PHE* 1.3 61.1 + - - +
500A VAL* 5.1 0.4 - - + -
529A TRP* 4.5 2.7 - - + -
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Residues in contact with PHE 499 (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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109A TRP* 3.7 22.4 - - + -
110A SER 3.2 12.1 - - - +
111A LEU* 3.8 14.8 - - + -
174A MET 3.8 0.2 - - - +
175A VAL* 3.4 5.4 - - - +
176A ALA* 2.7 52.7 + - + +
178A ASP* 3.7 27.8 - - + -
183A MET* 4.1 5.6 - - + -
208A TRP* 3.5 49.4 - + + -
246A ILE* 3.6 26.2 - - + -
250A VAL* 5.6 0.2 - - + -
497A GLN* 3.6 26.5 - - + -
498A LEU* 1.3 76.8 - - - +
500A VAL* 1.3 65.6 + - - +
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Residues in contact with VAL 500 (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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71A LEU* 3.3 37.7 - - + -
109A TRP* 3.6 2.0 - - - -
110A SER* 2.9 37.7 + - - +
112A VAL* 4.3 11.4 - - + -
145A ILE* 4.2 16.8 - - + -
173A LEU* 4.1 3.8 - - + -
174A MET 3.2 11.0 - - - +
175A VAL* 3.9 17.5 - - + -
205A PRO* 4.7 3.6 - - + -
498A LEU* 5.1 1.1 - - + -
499A PHE* 1.3 81.5 - - - +
501A LYS* 1.3 62.4 + - - +
527A PHE* 3.9 19.3 - - + -
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Residues in contact with LYS 501 (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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71A LEU* 4.4 5.4 - - - -
74A PRO* 3.9 7.2 - - + -
77A GLU* 2.9 35.2 + - - +
108A PRO* 3.4 35.0 - - - +
109A TRP* 3.5 34.5 - - + +
173A LEU* 3.5 5.6 - - - +
174A MET* 2.5 84.9 + - + +
247A GLU* 5.1 2.4 + - - +
500A VAL* 1.3 79.1 - - - +
502A VAL* 1.3 64.9 + - - +
504A PRO* 3.8 5.3 - - - +
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Residues in contact with VAL 502 (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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71A LEU* 4.0 33.5 - - + +
72A ASN 4.2 15.8 + - - +
73A MET* 4.2 14.1 - - + +
74A PRO* 4.5 5.3 - - - +
77A GLU* 3.9 3.3 - - - +
150A LEU* 3.8 20.2 - - + -
172A SER 4.2 3.1 - - - +
173A LEU* 4.7 2.5 - - - -
501A LYS* 1.3 86.6 + - - +
503A ALA* 1.3 76.6 + - - +
504A PRO 3.7 0.2 - - - -
523A THR* 3.9 22.4 - - + -
524A TYR* 4.5 2.0 - - - -
525A SER* 4.3 14.1 - - - +
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Residues in contact with ALA 503 (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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172A SER* 3.1 25.0 + - - +
174A MET* 3.0 31.2 - - + -
254A LEU* 4.4 10.8 - - + -
501A LYS 3.3 2.4 + - - -
502A VAL* 1.3 87.1 - - - +
504A PRO* 1.3 72.8 - - + +
505A ASN* 3.4 4.9 + - - +
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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