Contacts of the strand formed by residues 661 - 665 (chain A) in PDB entry 4JPB
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 ILE 661 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A VAL* 3.9 17.0 + - - +
653A ALA* 3.8 16.2 - - + -
654A ALA 3.5 5.4 - - - +
655A ILE* 4.2 8.1 - - + -
656A LEU* 4.7 1.6 - - - -
659A GLY 4.8 0.2 - - - +
660A SER* 1.3 82.7 + - - +
662A ALA* 1.3 75.7 + - - +
663A LEU* 4.2 9.9 - - + -
40W THR* 3.7 35.0 + - + +
52W VAL* 4.4 7.4 - - + +
53W ILE* 5.0 1.1 - - - -
54W ASN* 3.7 33.0 - - + +
59W ILE* 3.5 25.6 - - + -
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Residues in contact with ALA 662 (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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548A LEU* 5.2 0.7 - - + -
555A VAL* 3.2 31.0 - - + +
557A ALA* 4.4 17.7 - - + -
653A ALA* 3.1 4.9 - - - +
654A ALA* 2.7 38.2 + - + +
656A LEU* 4.1 18.4 - - + +
660A SER 4.0 0.6 + - - -
661A ILE* 1.3 78.3 - - - +
663A LEU* 1.3 59.8 + - - +
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Residues in contact with LEU 663 (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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555A VAL 3.2 6.6 + - - +
556A TYR* 3.3 18.6 - - + +
557A ALA 2.8 21.0 + - - -
640A LEU* 3.9 14.1 - - + -
650A PHE* 3.7 46.2 - - + -
652A GLY 3.5 4.0 - - - +
653A ALA* 3.7 21.1 - - + -
661A ILE* 4.2 9.6 - - + -
662A ALA* 1.3 76.5 - - - +
664A ILE* 1.3 63.6 + - - +
665A ILE 3.6 0.7 + - - -
40W THR* 5.1 6.5 - - + -
41W PRO 4.0 19.3 - - - +
42W VAL* 4.1 10.8 - - + -
52W VAL* 4.5 12.8 - - + -
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Residues in contact with ILE 664 (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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544A ILE* 5.0 8.3 - - + -
557A ALA* 3.3 29.6 - - + +
559A PRO* 3.9 14.1 - - + -
635A ILE* 4.1 10.3 - - + -
637A ILE* 4.6 20.9 - - + -
650A PHE* 3.3 6.3 - - - -
651A SER* 3.1 33.5 + - - +
652A GLY* 2.5 44.2 + - - +
653A ALA 3.5 20.0 - - - +
654A ALA* 3.8 10.3 - - + +
663A LEU* 1.3 70.8 - - - +
665A ILE* 1.3 73.1 + - - +
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Residues in contact with ILE 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A TYR* 3.7 28.7 - - + -
557A ALA 3.0 10.1 + - - +
558A ILE* 4.0 28.9 - - + -
559A PRO* 3.7 12.1 - - - +
595A LEU* 4.7 19.1 - - + -
599A LEU* 4.8 2.5 - - + -
624A ILE* 5.3 9.0 - - + -
649A GLU 3.8 3.6 - - - +
650A PHE* 3.9 20.9 - - + -
651A SER* 3.8 1.1 + - - -
663A LEU 3.6 0.6 + - - -
664A ILE* 1.3 84.0 - - - +
666A ASN* 1.3 66.2 + - - +
667A VAL* 3.6 13.3 + - + +
670A ILE* 3.7 26.2 - - + -
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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