Contacts of the strand formed by residues 647 - 652 (chain A) in PDB entry 4CAK
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 ALA 647 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A GLN* 1.1 141.9 - - - +
397A GLU* 3.7 2.0 - - + -
644A ALA* 3.7 13.7 - - + +
645A TYR 3.1 2.6 + - - -
646A GLU* 1.3 66.1 - - - +
648A GLU* 1.3 52.2 + - - +
689A LEU* 2.8 8.0 + - + -
690A GLY 3.3 3.1 - - - +
693A MET* 3.6 28.7 - - + -
723A ILE* 5.0 3.1 - - + -
724A ARG 3.4 8.5 - - - +
725A SER* 4.5 0.9 - - - +
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Residues in contact with GLU 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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298A VAL 2.4 15.8 - - - +
299A ASN* 2.0 43.7 - - - +
371A TYR* 2.2 16.9 - - - -
395A GLN* 1.3 136.6 + - - +
396A SER* 1.2 138.8 - - - +
397A GLU* 0.9 155.3 - - - +
398A GLY 2.4 23.4 - - - +
647A ALA* 1.3 66.2 - - - +
649A LEU* 1.3 8.6 - - - -
724A ARG 2.8 14.4 + - - -
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Residues in contact with LEU 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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299A ASN* 3.1 7.1 + - - +
332A LEU* 4.2 5.8 - - + +
396A SER 2.6 4.3 - - - -
397A GLU* 0.8 127.7 - - + +
614A LEU* 4.3 15.0 - - + -
635A MET* 3.5 40.4 - - + -
648A GLU 1.3 18.4 - - - -
650A ALA* 1.3 62.4 + - - +
651A VAL* 3.8 15.0 - - + -
685A VAL 3.4 1.2 - - - +
686A LEU* 3.2 1.4 - - - -
687A CYS* 3.1 25.4 + - + -
689A LEU* 4.3 1.1 - - + -
701A ILE* 3.8 19.3 - - + -
721A LEU* 4.5 2.5 - - + -
722A GLN 3.3 21.1 - - - +
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Residues in contact with ALA 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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299A ASN* 2.8 17.9 - - - +
301A ASP* 4.3 0.2 - - + -
335A ARG* 1.8 40.3 + - - +
396A SER 3.7 4.5 - - - +
649A LEU* 1.3 71.9 - - - +
651A VAL* 1.3 53.2 + - - +
652A HIS* 4.6 0.2 - - + -
686A LEU* 3.2 8.5 - - + -
722A GLN* 2.7 34.1 + - + +
724A ARG* 3.7 24.0 - - - +
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Residues in contact with VAL 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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301A ASP* 2.8 16.3 - - - +
332A LEU* 6.0 1.3 - - + -
335A ARG* 0.9 175.7 + - + +
633A LEU* 3.9 13.7 - - + -
635A MET* 4.1 4.3 - - + -
649A LEU* 3.8 28.7 - - + -
650A ALA* 1.3 68.0 - - - +
652A HIS* 1.3 21.9 + - - -
653A LEU* 4.3 0.2 - - + -
685A VAL* 2.8 27.5 + - + +
703A MET* 3.8 31.6 - - + -
719A PHE* 4.6 2.2 - - + -
720A GLN 4.0 1.3 - - - +
721A LEU* 4.2 12.3 - - + -
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Residues in contact with HIS 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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301A ASP* 4.4 1.5 - - + -
303A ARG* 1.8 39.9 - - - +
335A ARG* 1.0 224.6 + - - +
650A ALA* 4.6 0.4 - - + -
651A VAL 1.3 12.1 - - - -
653A LEU 1.3 43.7 - - - -
680A ASN* 4.7 2.9 + - + +
682A THR* 3.6 13.5 - - + -
684A VAL* 3.4 14.8 - - + +
718A SER 4.4 0.9 - - - +
719A PHE* 3.9 5.4 - - - -
720A GLN* 3.4 38.2 + - + +
722A GLN* 5.7 2.7 - - - -
724A ARG* 3.6 27.2 + - - -
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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