Contacts of the strand formed by residues 637 - 644 (chain A) in PDB entry 3BRF
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 637 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A MET 4.4 2.9 - - - +
628A PHE* 3.0 26.7 + - - +
630A ASN* 3.9 24.5 + - + +
633A THR* 3.6 22.5 + - - +
635A ASP* 3.6 6.3 + - + +
636A VAL* 1.3 78.1 - - - +
638A VAL* 1.3 60.6 + - - +
639A PRO* 4.1 3.5 - - - +
655A THR* 4.6 12.3 + - - +
656A PHE 3.2 5.6 - - - +
657A SER* 3.9 26.5 + - - +
659A LYS* 5.9 0.2 - - - +
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Residues in contact with VAL 638 (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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594A PHE* 2.9 31.4 - - + +
619A VAL* 4.7 7.0 - - + -
628A PHE* 3.6 30.5 - - + -
636A VAL* 4.5 7.2 - - + -
637A GLU* 1.3 74.6 - - - +
639A PRO* 1.4 63.1 - - + +
640A ILE 3.5 0.3 + - - -
655A THR* 3.1 3.9 - - - -
656A PHE* 2.5 62.4 + - + +
658A TYR* 3.7 31.2 - - + -
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Residues in contact with PRO 639 (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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203A MET* 5.9 0.2 - - - +
207A LEU* 4.5 19.7 - - + +
210A LYS* 4.7 15.5 - - - +
593A TRP 3.4 6.8 - - - +
594A PHE 3.2 16.5 - - - +
595A GLY* 3.8 2.8 - - - +
627A MET 5.2 2.7 - - - +
628A PHE* 3.7 30.7 - - + -
637A GLU 4.1 4.3 - - - +
638A VAL* 1.4 82.9 - - + +
640A ILE* 1.3 62.5 + - - +
641A SER* 3.9 2.1 + - - +
654A LEU 3.8 1.6 - - - +
655A THR* 3.8 20.1 - - + -
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Residues in contact with ILE 640 (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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210A LYS* 5.8 0.7 + - - -
565A VAL* 6.0 0.2 - - + -
568A LEU* 3.5 38.6 - - + -
579A VAL* 5.8 0.7 - - + -
581A LEU* 4.6 17.3 - - + -
592A VAL* 4.6 12.8 - - + -
593A TRP 3.6 2.5 - - - -
594A PHE* 4.8 24.0 - - + -
638A VAL 3.5 1.1 + - - +
639A PRO* 1.3 75.8 - - - +
641A SER* 1.3 74.6 + - - +
642A LEU* 5.7 0.9 - - + -
651A SER* 4.5 0.7 - - - -
652A SER* 2.8 36.1 + - - +
653A GLY 4.8 0.3 + - - -
654A LEU* 2.9 21.4 + - + +
655A THR 5.0 0.4 - - - -
656A PHE* 3.7 24.9 - - + +
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Residues in contact with SER 641 (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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203A MET* 3.7 30.5 - - - +
207A LEU* 4.5 9.2 - - - +
210A LYS* 4.9 1.0 + - - -
592A VAL* 3.3 7.3 - - - +
593A TRP* 2.7 38.9 + - - -
639A PRO* 4.8 2.0 + - - +
640A ILE* 1.3 78.5 + - - +
642A LEU* 1.3 64.7 + - - +
643A VAL* 4.2 0.4 - - - -
649A VAL* 3.9 13.8 - - - +
650A TYR 3.9 4.0 - - - -
651A SER* 3.8 15.2 - - - -
652A SER* 4.5 1.3 - - - +
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Residues in contact with LEU 642 (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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563A PRO* 3.8 36.8 - - + -
565A VAL* 3.9 18.4 - - + -
581A LEU* 4.3 13.9 - - + -
586A PHE* 3.9 21.8 - - + -
590A LEU* 4.4 13.0 - - + -
591A LYS 3.7 3.1 - - - +
592A VAL* 4.0 23.8 - - + +
609A LEU* 4.8 13.2 - - + -
640A ILE* 5.7 0.7 - - + -
641A SER* 1.3 80.2 - - - +
643A VAL* 1.3 56.0 + - - +
649A VAL* 3.6 1.0 - - - +
650A TYR* 2.6 46.4 + - + +
652A SER* 5.1 3.0 - - - +
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Residues in contact with VAL 643 (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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198A LEU* 3.7 30.1 - - + -
203A MET* 5.9 0.2 - - + -
589A ASN 4.0 0.2 - - - +
590A LEU* 3.6 7.2 - - - +
591A LYS* 3.1 27.4 + - + +
593A TRP* 2.9 48.0 - - + +
641A SER* 5.7 0.7 - - - -
642A LEU* 1.3 75.3 - - - +
644A ARG* 1.3 75.4 + - - +
645A ASP 4.0 0.3 + - - -
647A GLY 4.3 3.1 - - - -
648A VAL 3.4 17.5 - - - +
649A VAL* 4.1 9.0 - - + -
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Residues in contact with ARG 644 (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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198A LEU 5.3 1.4 + - - -
555A VAL* 3.9 8.9 - - - +
557A ASN* 4.0 5.9 + - - +
558A PRO 2.9 28.4 + - - -
559A ILE* 3.4 10.1 + - - +
560A SER 4.0 6.3 + - - -
561A PRO* 5.3 2.2 + - - +
589A ASN* 3.5 36.3 - - + +
590A LEU* 3.7 9.2 - - + +
643A VAL* 1.3 84.6 - - - +
645A ASP* 1.3 63.3 + - - +
646A ASP* 2.6 48.8 + - + +
647A GLY* 2.9 18.5 + - - -
648A VAL* 2.8 27.4 + - + +
650A TYR* 3.3 26.8 + - + -
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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