Contacts of the strand formed by residues 618 - 626 (chain A) in PDB entry 1EX0
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 618 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A LEU* 3.7 23.1 - - + -
358A GLY* 5.4 2.2 - - - +
441A TYR* 5.1 0.9 - - + -
453A GLU* 3.7 26.0 + - + -
454A ASN* 2.9 28.9 + - - +
609A THR* 5.5 1.8 - - - -
610A ALA 3.4 8.1 - - - +
611A ARG* 3.0 46.7 - - - +
616A ARG 3.6 0.2 + - - -
617A ASP* 1.3 76.4 - - - +
619A LEU* 1.3 81.2 + - - +
620A ALA* 4.4 6.7 - - + -
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Residues in contact with LEU 619 (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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454A ASN* 4.9 0.4 - - - +
518A VAL* 3.1 49.8 - - + +
520A MET* 3.5 42.6 - - + +
539A PHE* 4.3 8.5 - - + -
549A ILE* 4.7 2.2 - - + -
609A THR* 3.4 1.7 - - - -
610A ALA* 2.9 36.2 + - + +
612A ILE* 4.2 19.3 - - + -
617A ASP* 5.7 1.3 - - + -
618A VAL* 1.3 83.8 - - - +
620A ALA* 1.3 65.6 + - - +
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Residues in contact with ALA 620 (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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441A TYR* 3.6 46.0 + - + -
454A ASN* 4.8 5.1 + - - +
520A MET* 3.5 3.6 - - - +
608A VAL 3.5 6.1 - - - -
609A THR* 3.8 11.7 - - + -
618A VAL* 4.4 6.3 - - + -
619A LEU* 1.3 80.1 - - - +
621A LYS* 1.3 71.7 + - - +
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Residues in contact with LYS 621 (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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441A TYR* 4.4 3.2 + - - -
456A ASP* 5.8 1.1 - - - +
520A MET* 4.0 25.4 - - + +
521A ASP* 3.5 32.1 + - - +
522A PHE* 3.7 22.9 - - + +
607A PHE* 3.7 3.3 - - - -
608A VAL 2.9 29.6 + - - +
620A ALA* 1.3 79.8 - - - +
622A GLN* 1.3 70.5 + - - +
623A LYS* 4.1 10.5 - - - +
1330A PO4 2.9 45.5 + - - +
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Residues in contact with GLN 622 (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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350A MET* 5.8 2.7 - - - +
352A ILE* 3.6 19.0 - - - +
369A VAL* 5.3 6.1 - - - +
439A LEU* 3.7 15.5 - - + +
441A TYR* 3.1 25.9 + - - +
456A ASP* 5.9 0.6 + - - -
459A HIS* 4.3 27.3 + - + +
522A PHE* 3.9 0.7 - - - -
605A HIS* 2.8 28.5 + - - +
606A PHE 3.3 5.8 - - - -
607A PHE* 3.3 34.6 - - + -
621A LYS* 1.3 78.6 - - - +
623A LYS* 1.3 80.2 + - - +
1330A PO4 4.4 5.9 + - - -
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Residues in contact with LYS 623 (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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218A ASN* 4.6 19.0 - - - +
339A PHE* 5.3 5.4 - - - -
459A HIS* 5.6 0.2 - - - -
521A ASP* 3.6 18.4 + - - -
522A PHE* 3.1 54.2 + - + +
523A GLU* 5.1 3.3 - - - +
524A VAL* 4.0 15.5 - - + +
605A HIS* 3.5 6.6 - - - -
606A PHE* 2.9 34.0 + - - -
621A LYS* 4.1 15.2 - - - +
622A GLN* 1.3 84.4 + - - +
624A SER* 1.3 63.4 + - - +
1330A PO4 4.6 7.5 + - - -
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Residues in contact with SER 624 (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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216A GLU* 3.0 31.7 + - - +
218A ASN* 4.8 4.3 + - - +
339A PHE* 3.8 20.5 - - - -
371A ASN* 2.6 38.7 + - - -
524A VAL* 5.7 0.6 - - - +
604A LEU 3.4 9.3 + - - -
605A HIS* 3.6 18.2 - - - +
606A PHE* 4.8 0.2 - - - -
623A LYS* 1.3 77.9 - - - +
625A THR* 1.3 64.7 + - - +
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Residues in contact with THR 625 (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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216A GLU* 3.7 7.2 - - - -
371A ASN* 5.0 0.2 - - - +
524A VAL* 3.8 21.5 + - + +
525A GLU 4.2 5.0 + - - +
526A ASN* 3.7 19.3 + - - -
527A ALA 6.3 0.4 - - - +
533A PHE* 5.0 7.2 - - + -
603A SER* 3.4 3.3 - - - -
604A LEU* 2.7 64.5 + - + +
606A PHE* 3.7 18.6 - - + -
624A SER* 1.3 79.0 + - - +
626A VAL* 1.3 66.2 + - - +
627A LEU* 4.9 2.5 - - + +
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Residues in contact with VAL 626 (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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215A GLY* 4.0 38.4 - - - +
216A GLU* 4.1 9.9 + - + +
219A ASP* 3.4 27.8 - - - +
221A LYS* 4.3 9.6 - - + -
371A ASN* 4.8 2.0 - - - +
372A TYR* 6.5 0.2 - - + -
526A ASN* 4.8 2.4 + - - -
527A ALA 4.3 7.4 + - - +
601A GLN* 3.8 20.9 - - + +
602A ALA 3.3 4.7 - - - -
603A SER* 4.0 14.8 - - - +
625A THR* 1.3 82.4 - - - +
627A LEU* 1.3 68.0 + - - +
628A THR 3.9 0.3 + - - -
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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