Contacts of the strand formed by residues 621 - 625 (chain B) in PDB entry 4P3N
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 VAL 621 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614B PHE* 5.0 0.2 - - + -
619B ARG 3.7 0.8 - - - -
620B GLN* 1.3 89.8 - - + +
622B MET* 1.3 60.5 + - - +
623B VAL* 3.9 17.5 - - + -
641B PHE* 4.3 13.5 - - + -
646B PHE* 4.6 6.3 - - + -
647B MET 3.0 3.4 + - - +
648B ALA* 3.5 20.1 - - + -
649B ASP 2.9 24.6 + - - -
670B TYR* 3.2 12.8 - - - -
672B PHE* 3.3 7.9 - - + -
674B LEU* 3.7 28.7 - - + -
708B LEU* 4.3 23.8 - - + -
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Residues in contact with MET 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B VAL* 1.3 72.5 - - - +
623B VAL* 1.3 68.8 + - - +
624B VAL* 3.6 4.9 + - + -
649B ASP* 3.7 21.8 - - + -
650B ILE 3.7 29.2 - - - +
651B ASP* 3.8 19.1 - - + +
665B ALA* 3.8 18.2 - - + -
670B TYR* 3.6 32.5 - - + +
672B PHE 2.9 8.1 + - - -
673B ILE* 3.4 21.1 - - + +
674B LEU 2.9 25.4 + - - +
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Residues in contact with VAL 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B VAL* 3.9 16.4 - - + -
622B MET* 1.3 74.8 - - - +
624B VAL* 1.3 61.1 + - - +
634B ALA* 3.6 35.4 - - + +
637B VAL* 4.1 17.3 - - + -
638B ARG* 3.7 29.8 - - + +
641B PHE* 5.5 0.2 - - + -
649B ASP 2.9 15.6 + - - +
650B ILE* 3.2 11.3 - - + +
651B ASP 2.9 25.5 + - - -
674B LEU* 3.4 13.0 - - + +
676B VAL* 4.3 7.6 - - + -
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Residues in contact with VAL 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B MET* 4.4 13.7 - - + +
623B VAL* 1.3 79.0 - - - +
625B PRO* 1.3 78.7 - - + +
651B ASP* 4.0 16.6 - - + -
658B LEU* 3.7 20.6 - - + -
661B LYS* 3.5 39.9 - - + +
662B ILE* 5.0 0.7 - - + +
665B ALA* 5.8 0.4 - - + -
673B ILE* 4.6 10.5 - - + -
674B LEU 2.9 9.5 + - - +
675B VAL* 3.3 8.9 - - + +
676B VAL* 2.9 28.5 + - - +
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Residues in contact with PRO 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B VAL 4.1 2.9 - - - +
624B VAL* 1.3 101.7 - - + +
626B VAL* 1.3 63.9 + - - +
627B GLY 3.5 18.6 - - - +
630B CYS* 4.2 10.8 - - + -
631B ASP* 3.4 20.6 - - - +
634B ALA* 4.1 15.9 - - + -
651B ASP 3.1 22.2 - - - +
652B LEU* 3.8 9.6 - - + -
658B LEU* 4.3 3.6 - - - +
661B LYS* 4.6 10.8 + - - +
676B VAL* 3.4 9.9 - - + +
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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