Contacts of the strand formed by residues 599 - 608 (chain A) in PDB entry 4I1R
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 GLN 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591A CYS* 3.7 23.8 - - + +
592A LEU 3.5 20.6 - - - +
593A LYS* 4.1 20.9 - - + +
597A GLY 3.4 5.8 + - - +
598A VAL* 1.3 71.3 - - - +
600A ILE* 1.4 64.6 + - - +
618A ILE 3.9 0.5 - - - -
619A VAL* 3.0 48.3 + - + +
620A TYR* 3.4 20.4 + - + +
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Residues in contact with ILE 600 (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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590A MET 4.0 0.2 - - - +
591A CYS* 3.2 8.0 - - - +
592A LEU* 2.9 39.8 + - + +
594A PHE* 3.7 29.4 - - + -
598A VAL* 3.8 25.6 - - + -
599A GLN* 1.4 73.0 - - - +
601A GLN* 1.3 72.8 + - - +
602A LEU* 5.3 6.5 - - + -
616A THR* 4.6 5.6 - - + -
617A SER 3.4 9.4 - - - +
618A ILE* 3.9 21.3 - - + -
619A VAL* 4.8 1.6 - - - -
628A CYS* 5.6 0.9 - - - -
630A ALA* 3.6 31.6 - - + +
686A VAL* 4.9 5.4 - - + -
688A LEU* 4.0 8.1 - - + -
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Residues in contact with GLN 601 (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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589A SER* 3.2 29.1 + - - -
590A MET 3.6 6.5 + - - -
591A CYS* 3.0 32.9 - - - -
600A ILE* 1.3 76.7 - - - +
602A LEU* 1.3 59.9 + - - +
603A GLY 4.0 0.7 - - - -
615A TYR* 3.6 10.3 - - + +
616A THR* 3.4 7.4 - - - -
617A SER* 2.8 51.2 + - - +
619A VAL* 4.6 16.3 - - + +
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Residues in contact with LEU 602 (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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589A SER* 3.3 7.9 + - - -
590A MET* 2.5 58.0 + - + +
592A LEU* 3.8 28.0 - - + -
600A ILE* 5.3 3.4 - - + -
601A GLN* 1.3 74.1 - - - +
603A GLY* 1.3 59.7 - - - +
604A PHE* 3.7 20.9 - - + -
614A ILE* 3.8 21.8 - - + -
615A TYR 3.5 4.5 - - - +
616A THR* 4.8 5.4 - - + -
632A VAL* 4.8 3.1 - - + -
684A PHE* 3.7 26.5 - - + -
686A VAL* 4.0 21.1 - - + -
705A VAL* 4.7 3.4 - - + -
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Residues in contact with GLY 603 (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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589A SER* 4.1 9.9 - - - -
601A GLN* 4.0 1.4 - - - +
602A LEU* 1.3 73.0 - - - +
604A PHE* 1.3 76.5 + - - -
614A ILE* 3.7 1.9 - - - +
615A TYR* 2.8 60.7 + - - +
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Residues in contact with PHE 604 (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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586A LEU* 3.5 24.2 - - + +
587A PRO* 3.2 38.1 - - + +
588A GLU 3.8 16.8 - - - -
589A SER* 4.5 2.3 - - - +
590A MET* 4.3 7.6 - - + -
602A LEU* 3.7 37.9 - - + -
603A GLY* 1.3 78.1 - - - -
605A ALA* 1.3 61.4 + - - +
612A MET* 3.8 16.6 - - + -
613A ILE 3.5 4.5 - - - +
614A ILE* 3.9 22.9 - - + -
615A TYR* 3.5 12.4 + - - -
684A PHE* 5.1 1.1 - + - -
707A VAL* 3.4 30.5 - - + -
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Residues in contact with ALA 605 (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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586A LEU* 3.8 8.1 - - - -
604A PHE* 1.3 76.4 - - - +
606A ALA* 1.3 60.6 + - - +
612A MET* 3.5 7.3 - - - +
613A ILE* 2.9 37.8 + - + +
615A TYR* 4.8 0.7 - - + -
658A LEU* 3.8 17.0 - - + -
663A LEU* 3.8 28.5 - - + -
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Residues in contact with ALA 606 (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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367A TYR* 4.9 2.8 + - - -
586A LEU* 3.9 22.4 - - + +
605A ALA* 1.3 73.4 - - - +
607A GLU* 1.3 62.5 + - - +
608A PHE 4.8 3.4 - - - +
611A VAL 4.1 2.9 - - - -
658A LEU* 3.6 17.2 - - - +
711A LEU* 4.1 17.7 - - + -
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Residues in contact with GLU 607 (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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363A LEU* 3.8 0.9 - - - +
367A TYR* 3.4 30.1 - - + -
370A THR* 6.2 0.2 - - - +
374A ARG* 5.8 1.6 + - - -
382A SER* 4.6 0.9 + - - -
605A ALA 4.0 0.6 + - - -
606A ALA* 1.3 75.5 - - - +
608A PHE* 1.4 91.9 + - + +
611A VAL* 3.0 15.2 + - + +
613A ILE* 3.2 17.9 - - + +
656A SER* 3.1 10.5 - - - -
657A TYR* 2.8 29.8 + - - +
658A LEU* 3.9 13.2 - - + -
671A ARG* 2.7 34.2 + - - -
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Residues in contact with PHE 608 (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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363A LEU* 3.2 35.2 - - + -
366A VAL* 3.7 13.9 - - + -
367A TYR* 3.4 36.6 - + + -
374A ARG* 6.3 1.6 - - - -
382A SER* 3.2 30.3 - - - +
384A LEU* 3.7 21.8 - - + -
584A HIS* 5.5 1.3 + - - -
606A ALA* 4.8 2.9 - - - +
607A GLU* 1.4 111.1 + - + +
609A SER* 1.3 65.7 + - - +
610A ASN* 3.2 14.4 - - - +
611A VAL* 3.2 29.3 + - + +
711A LEU* 3.8 9.0 - - - +
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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