Contacts of the strand formed by residues 647 - 654 (chain A) in PDB entry 4P5Q
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 647 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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639A ARG* 3.6 34.4 + - + +
640A LEU 3.4 5.4 - - - +
641A LYS* 2.7 50.0 + - + +
645A LYS 3.4 1.1 + - - +
646A LYS* 1.3 80.5 - - - +
648A ILE* 1.3 63.7 + - - +
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Residues in contact with ILE 648 (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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639A ARG* 3.3 11.4 - - - +
640A LEU* 2.9 42.5 + - + +
642A LEU* 4.1 28.5 - - + -
646A LYS* 4.1 18.6 - - + +
647A GLU* 1.3 78.4 - - - +
649A SER* 1.3 64.7 + - - +
650A VAL* 4.0 15.5 - - + -
686A GLU* 3.5 37.0 - - + +
700A GLU* 6.0 1.3 - - + -
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Residues in contact with SER 649 (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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638A GLY 3.5 9.0 - - - -
639A ARG* 2.8 27.7 + - - +
648A ILE* 1.3 79.1 - - - +
650A VAL* 1.3 65.1 + - - +
700A GLU* 4.4 2.4 - - - +
701A TYR* 3.5 40.0 + - - +
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Residues in contact with VAL 650 (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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621A ILE* 5.4 0.9 - - + -
637A SER* 3.5 3.6 - - - -
638A GLY 2.9 45.0 + - - +
639A ARG 3.8 12.8 - - - +
640A LEU* 3.8 17.3 - - + +
648A ILE* 4.0 14.1 - - + -
649A SER* 1.3 82.3 - - - +
651A ALA* 1.3 60.8 + - - +
652A ILE* 4.0 12.8 - - + -
686A GLU* 4.2 5.4 - - + -
698A VAL* 3.6 27.6 - - + -
699A THR 3.2 14.4 - - - +
700A GLU* 4.9 0.2 - - - -
701A TYR* 3.8 11.4 - - - -
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Residues in contact with ALA 651 (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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635A VAL* 4.9 0.9 - - + -
636A CYS 3.5 7.9 - - - +
637A SER* 4.6 0.9 - - - +
650A VAL* 1.3 74.0 - - - +
652A ILE* 1.3 62.7 + - - +
698A VAL* 3.5 3.8 - - - +
699A THR* 2.8 32.4 + - - +
700A GLU 4.0 0.4 - - - +
701A TYR* 4.0 3.4 - - + +
1001A Q0B 3.2 64.4 - - + +
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Residues in contact with ILE 652 (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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621A ILE* 3.8 15.5 - - + -
622A SER 4.0 9.0 - - - +
623A ILE* 3.6 28.3 - - + -
634A GLU 3.9 0.3 - - - +
635A VAL* 3.4 2.7 - - - +
636A CYS* 2.7 43.5 + - + +
637A SER 4.2 2.0 - - - -
638A GLY 4.1 10.8 - - - +
650A VAL* 4.0 18.6 - - + -
651A ALA* 1.3 80.3 - - - +
653A LYS* 1.3 63.3 + - - +
654A THR* 3.8 8.8 + - + +
696A MET* 3.6 39.5 - - + -
697A ILE 3.5 3.8 - - - +
698A VAL* 4.4 9.9 - - + -
1001A Q0B 4.2 0.4 - - - -
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Residues in contact with LYS 653 (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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630A GLY* 5.6 3.5 - - - -
631A GLU* 5.6 7.2 - - - +
632A PHE* 5.6 6.9 - - - +
633A GLY 6.1 0.2 - - - +
634A GLU 3.9 2.9 - - - +
635A VAL* 3.8 22.8 - - + +
652A ILE* 1.3 71.5 - - - +
654A THR* 1.3 61.6 + - - +
667A PHE* 3.5 27.4 - - + -
670A GLU* 3.3 26.1 + - - +
696A MET* 3.2 6.8 - - - +
697A ILE* 2.9 40.4 + - + +
1001A Q0B 3.3 54.1 + - + +
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Residues in contact with THR 654 (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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623A ILE* 5.4 4.5 - - + -
632A PHE 3.6 1.7 - - - +
633A GLY* 3.3 22.2 + - - -
634A GLU* 2.9 35.9 + - - +
636A CYS* 4.5 13.2 - - - -
652A ILE* 4.3 17.9 - - + +
653A LYS* 1.3 78.4 - - - +
655A LEU* 1.3 62.2 + - - +
656A LYS* 5.4 0.9 - - - -
667A PHE* 3.8 8.1 - - - -
694A PRO* 4.4 15.9 - - + -
695A VAL 3.5 6.3 - - - -
696A MET* 4.3 10.1 - - + -
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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