Contacts of the strand formed by residues 684 - 690 (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 VAL 684 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A ASN* 3.5 4.9 - - - +
301A ASP* 0.9 221.2 - - + +
303A ARG* 0.8 163.8 - - - +
333A GLN 3.5 0.4 - - - -
335A ARG* 3.8 7.2 - - - +
651A VAL 3.7 4.7 - - - +
652A HIS* 3.4 9.2 - - + -
680A ASN* 3.6 0.9 - - + -
682A THR 3.2 7.0 - - - +
683A ARG 1.3 15.6 - - - -
685A VAL* 1.3 47.6 + - - +
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Residues in contact with VAL 685 (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* 2.2 21.5 + - - -
301A ASP* 2.2 10.3 + - - -
305A ASP* 2.9 2.5 - - - -
332A LEU* 1.9 74.3 - - + +
333A GLN* 1.0 100.6 + - + +
334A PRO* 2.1 17.9 - - + +
649A LEU 3.4 2.3 - - - +
651A VAL* 2.8 28.6 + - + +
659A TYR* 3.8 0.7 - - + -
684A VAL* 1.3 65.7 - - - +
686A LEU* 1.3 51.4 + - - +
687A CYS 4.2 0.2 + - - -
703A MET* 4.3 2.9 - - - -
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Residues in contact with LEU 686 (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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297A ASP* 2.7 17.9 - - - +
298A VAL* 2.3 22.6 - - - +
299A ASN* 1.3 356.7 + - + +
300A GLY* 1.1 49.6 - - - +
301A ASP* 2.8 10.5 - - - +
305A ASP* 2.7 9.1 + - - +
332A LEU* 1.5 31.3 - - - +
650A ALA* 3.2 14.6 - - + -
675A ASN 3.0 0.5 + - - -
685A VAL* 1.3 64.5 - - - +
687A CYS* 1.3 48.0 - - - +
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Residues in contact with CYS 687 (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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330A LEU* 4.1 0.7 - - + -
332A LEU* 1.0 132.0 - - + +
344A SER* 2.6 11.2 - - - -
397A GLU 0.8 92.6 - - - +
398A GLY* 1.0 81.5 + - - +
635A MET* 6.5 0.2 - - - -
649A LEU* 3.1 7.4 + - + +
662A ALA* 4.5 0.4 - - - -
672A LEU* 4.2 10.1 - - + -
673A ILE 3.6 2.2 - - - -
674A CYS* 2.0 24.2 - - - -
686A LEU* 1.3 64.6 - - - +
688A GLU 1.3 17.3 - - - +
701A ILE* 5.4 2.2 - - + -
703A MET* 5.1 2.9 - - - -
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Residues in contact with GLU 688 (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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345A LEU* 1.9 40.1 - - + +
392A PHE* 4.5 0.9 - - - +
393A LEU 2.7 10.9 - - - +
394A GLY* 4.3 0.2 - - - -
397A GLU 3.1 5.4 - - - +
398A GLY* 1.1 92.3 - - - +
399A LEU* 0.6 415.8 - - + +
400A ARG 2.6 14.5 + - - +
401A SER 3.8 0.2 + - - -
647A ALA 3.8 0.4 - - - -
672A LEU* 3.7 0.3 - - - +
673A ILE* 3.2 7.7 + - - +
687A CYS* 1.3 17.4 - - - +
689A LEU* 1.3 57.3 + - - +
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Residues in contact with LEU 689 (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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345A LEU* 5.6 0.7 - - - -
395A GLN* 2.5 8.6 + - - +
397A GLU* 1.7 75.8 - - + +
399A LEU 4.2 0.2 - - - -
401A SER* 5.5 2.2 - - - -
637A ALA* 4.2 9.6 - - + -
647A ALA* 2.8 10.6 + - + +
672A LEU* 5.3 2.2 - - + -
688A GLU* 1.3 76.1 - - - +
690A GLY* 1.3 54.3 + - - +
693A MET* 4.4 16.8 - - + +
699A ILE* 3.1 41.4 - - + +
701A ILE* 3.3 26.5 - - + -
723A ILE* 3.5 13.7 - - + -
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Residues in contact with GLY 690 (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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395A GLN* 1.5 58.8 + - - -
399A LEU 3.7 1.2 + - - -
400A ARG* 3.5 6.5 - - - -
401A SER* 4.4 6.1 - - - -
644A ALA 3.7 0.2 - - - +
647A ALA* 3.3 2.6 - - - +
688A GLU 3.6 1.4 - - - -
689A LEU* 1.3 71.4 - - - +
691A ASN* 1.3 57.3 + - - -
692A PRO 3.4 13.2 - - - -
693A MET* 3.4 4.8 + - - -
465B GLY 4.6 2.9 - - - -
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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