Contacts of the strand formed by residues 599 - 603 (chain A) in PDB entry 7REQ
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 ARG 599 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A ARG* 4.0 21.5 - - - +
597A ARG 4.3 2.2 + - - +
598A PRO* 1.3 73.1 - - - +
600A ILE* 1.3 65.7 - - - +
626A PHE* 5.4 0.2 - - - -
627A ASP* 3.2 40.8 + - + +
628A VAL 6.1 0.2 - - - -
629A ASP* 3.5 26.4 + - - +
647A ALA* 3.3 29.0 + - - +
649A VAL* 3.5 24.5 - - + +
650A HIS* 3.0 30.0 + - - +
651A VAL* 3.4 9.3 + - - +
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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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599A ARG* 1.3 76.5 - - - +
601A LEU* 1.3 71.7 + - - +
602A LEU* 3.8 24.6 + - + -
621A TYR* 4.3 21.1 - - + -
626A PHE* 4.3 9.2 - - + -
627A ASP 2.9 10.5 + - - +
628A VAL* 3.6 11.9 - - + +
629A ASP* 3.0 25.5 + - - +
649A VAL* 4.2 4.0 - - - -
651A VAL* 3.2 31.0 - - + +
653A GLY* 3.7 13.2 - - - +
683A THR* 4.8 0.4 - - - +
718A LEU* 3.8 19.3 - - + -
1800A B12 4.1 7.6 - - + -
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Residues in contact with LEU 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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600A ILE* 1.3 73.2 - - - +
602A LEU* 1.3 64.8 + - - +
603A ALA* 3.5 3.2 + - + +
629A ASP* 3.6 22.7 - - + +
631A GLY* 4.0 12.6 - - - +
635A GLN* 5.3 0.2 - - - +
640A THR* 3.5 42.2 - - + +
643A GLN* 3.7 32.3 - - + +
644A ALA* 3.8 18.8 - - + +
649A VAL* 4.0 18.8 - - + +
651A VAL 3.1 8.5 + - - +
652A VAL* 3.5 6.3 - - + +
653A GLY 2.8 25.3 + - - -
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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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600A ILE* 3.8 23.3 - - + -
601A LEU* 1.3 70.8 - - - +
603A ALA* 1.3 57.3 + - - +
614A GLN* 2.7 50.0 + - + +
617A ILE* 3.6 11.2 - - + +
618A ALA* 3.4 43.1 - - + +
621A TYR* 5.5 0.9 - - + -
628A VAL* 3.9 13.7 - - + -
629A ASP 3.0 12.0 + - - +
630A VAL* 4.9 1.8 - - - -
631A GLY 3.0 13.7 + - - -
653A GLY 3.4 5.6 - - - +
655A SER* 6.3 0.4 - - - -
1800A B12 3.6 32.5 - - + -
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Residues in contact with ALA 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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601A LEU* 3.5 4.4 + - + -
602A LEU* 1.3 74.3 - - - +
604A LYS* 1.3 65.6 - - - +
605A MET* 4.0 6.3 + - + -
614A GLN* 4.5 0.4 - - - -
631A GLY* 5.0 1.3 - - - -
635A GLN* 4.3 7.6 - - - +
640A THR* 3.5 33.7 - - + +
652A VAL* 4.0 12.6 - - + -
653A GLY 3.0 10.6 + - - +
654A VAL* 3.7 7.5 - - + +
655A SER* 3.0 31.9 + - - +
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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