Contacts of the strand formed by residues 591 - 599 (chain A) in PDB entry 4Z4H
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 591 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586A VAL* 4.1 18.6 - - + +
587A PHE* 4.3 5.4 - - + -
589A GLN 3.7 6.1 - - - +
590A PRO* 1.3 74.3 - - - +
592A ILE* 1.3 64.6 + - - +
593A PHE* 3.9 26.4 - - + -
617A SER* 4.3 2.9 + - - -
619A ASP 5.0 1.2 - - - +
653A PHE* 3.6 15.5 - - - -
661A PRO* 4.3 0.9 - - - -
663A ARG* 3.6 23.6 - - + +
665A ILE* 3.8 28.9 - - + -
903A IPH 3.4 29.5 + - + -
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Residues in contact with ILE 592 (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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591A VAL* 1.3 77.7 - - - +
593A PHE* 1.3 65.6 + - - +
594A LEU* 3.8 21.5 - - + -
616A GLY* 4.4 4.9 - - - -
617A SER* 3.4 30.1 - - - +
618A MET* 4.5 0.7 - - + -
649A LEU* 4.4 13.2 - - + +
650A LEU* 4.5 9.0 - - + -
653A PHE* 3.6 23.1 - - + -
661A PRO* 3.9 17.2 - - + +
663A ARG 3.2 2.8 + - - -
664A ILE* 3.8 33.0 - - + -
665A ILE 3.1 21.8 + - - +
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Residues in contact with PHE 593 (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 VAL* 4.8 2.5 - - + -
587A PHE* 3.7 38.4 - + - -
591A VAL* 3.9 26.0 - - + -
592A ILE* 1.3 74.0 - - - +
594A LEU* 1.3 62.6 + - - +
616A GLY* 3.4 3.6 - - - -
617A SER* 3.0 38.3 + - - +
622A PRO* 4.0 14.4 - - + -
625A TYR* 3.7 19.3 - - + +
665A ILE* 3.5 30.5 - - + -
667A TYR* 4.6 1.8 - + + -
782A LEU* 3.9 17.0 - - + -
786A LEU* 3.7 30.1 - - + -
802A PRO* 4.7 6.3 - - + -
903A IPH 6.2 0.2 - + - -
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Residues in contact with LEU 594 (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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592A ILE* 3.8 20.4 - - + -
593A PHE* 1.3 73.9 - - - +
595A GLY* 1.3 59.9 + - - +
614A VAL* 4.4 7.2 - - + -
615A VAL 3.2 4.0 - - - +
616A GLY* 3.6 24.0 - - - -
646A VAL* 4.0 31.2 - - + -
649A LEU* 4.2 11.4 - - + -
664A ILE* 4.2 21.8 - - + -
665A ILE 2.7 14.3 + - - +
666A PHE* 3.7 30.5 - - + -
667A TYR* 2.8 32.7 + - - +
687A ILE* 5.3 0.7 - - + -
802A PRO* 4.1 3.4 - - - -
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Residues in contact with GLY 595 (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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594A LEU* 1.3 73.6 - - - +
596A ALA* 1.3 61.3 + - - +
614A VAL* 3.2 6.4 - - - +
615A VAL 2.8 33.7 + - - -
667A TYR* 3.6 5.6 - - - -
802A PRO* 3.6 29.4 - - - +
803A ALA 4.1 1.3 - - - -
806A ALA* 3.8 9.1 - - - +
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Residues in contact with ALA 596 (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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595A GLY* 1.3 75.0 - - - +
597A ASP* 1.3 63.4 + - - +
613A ALA 3.3 6.7 - - - +
614A VAL* 4.2 5.2 - - + -
639A ILE* 3.7 19.1 - - + -
666A PHE* 3.7 32.8 - - + -
667A TYR 3.1 7.1 + - - +
668A ARG* 3.9 8.3 - - - -
669A ASP* 3.0 27.2 + - - +
803A ALA* 4.9 1.6 - - - +
806A ALA* 3.9 3.4 - - - +
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Residues in contact with ASP 597 (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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596A ALA* 1.3 76.9 - - - +
598A VAL* 1.3 63.6 + - - +
599A THR* 3.1 24.6 + - - -
611A ILE 3.7 0.7 - - - +
612A ALA* 3.5 2.3 - - - +
613A ALA* 2.9 33.4 + - - +
639A ILE* 4.6 1.6 - - - +
668A ARG* 4.2 5.6 - - - +
669A ASP* 3.0 21.7 - - + +
806A ALA* 3.8 18.6 - - + +
807A HIS* 3.3 28.8 + - + +
810A ALA* 4.4 1.9 - - - +
901A MG 2.7 22.3 - - - -
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Residues in contact with VAL 598 (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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597A ASP* 1.3 83.0 + - - +
599A THR* 1.3 57.8 + - - +
600A HIS* 3.4 31.5 + - + +
610A SER* 3.9 10.5 - - - -
611A ILE 3.2 11.2 - - - +
612A ALA* 4.1 8.1 - - + -
632A GLN* 4.2 3.8 - - - +
636A GLN 3.7 7.6 - - - +
637A GLU* 3.2 34.3 + - - +
639A ILE* 3.8 18.4 - - + -
668A ARG* 3.9 7.4 - - - +
901A MG 2.1 33.3 - - - -
10B C 3.9 1.4 - - - +
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Residues in contact with THR 599 (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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597A ASP* 3.1 16.5 + - - -
598A VAL* 1.3 71.7 - - - +
600A HIS* 1.3 71.2 + - - +
610A SER* 3.6 0.3 - - - -
611A ILE* 2.9 33.1 + - - -
807A HIS* 4.8 3.6 + - - -
810A ALA* 3.4 22.0 - - - +
811A PHE* 4.0 26.6 - - + -
814A ARG* 3.2 18.4 + - + +
901A MG 4.2 0.2 - - - -
10B C 3.4 20.0 + - + +
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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