Contacts of the strand formed by residues 609 - 614 (chain A) in PDB entry 5ULM
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 609 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A ILE* 4.1 20.0 - - + -
604A PHE* 4.2 12.3 - - + -
605A SER 3.5 15.9 - - - +
606A ALA* 3.1 19.6 + - - +
607A SER 4.2 4.7 - - - +
608A SER* 1.3 78.4 - - - +
610A ARG* 1.3 63.0 + - - +
611A GLY 3.8 8.3 - - - +
624A LEU* 3.6 26.2 - - + -
625A TYR 3.8 5.8 - - - +
626A VAL* 4.5 3.8 - - + +
627A LEU* 5.2 0.9 - - - -
650A VAL* 3.9 18.6 - - + -
653A ILE* 5.4 1.1 - - + -
654A THR* 4.0 14.6 - - + +
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Residues in contact with ARG 610 (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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608A SER 3.6 3.6 + - - -
609A VAL* 1.3 74.0 - - - +
611A GLY* 1.3 57.6 + - - +
625A TYR* 2.8 57.4 + - + +
626A VAL* 4.6 4.7 + - - +
627A LEU* 4.6 23.9 - - + +
632A ASP* 4.4 5.1 + - - -
654A THR* 4.9 5.9 + - - +
450B PHE* 5.8 3.0 - - - -
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Residues in contact with GLY 611 (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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609A VAL* 3.6 8.1 - - - +
610A ARG* 1.3 82.7 - - - +
612A VAL* 1.3 68.5 - - - +
624A LEU* 3.7 2.9 - - - +
625A TYR* 2.9 35.2 + - - +
650A VAL* 5.2 0.7 - - - -
651A ASN* 5.7 2.2 - - - -
654A THR* 5.0 7.9 - - - -
450B PHE* 5.5 8.3 - - - -
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Residues in contact with VAL 612 (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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611A GLY* 1.3 77.0 - - - +
613A SER* 1.3 62.6 + - - +
622A CYS* 3.8 7.0 - - - -
623A PHE 3.2 14.8 - - - +
624A LEU* 3.9 11.0 - - + -
625A TYR* 4.1 3.8 - - - -
646A PHE* 4.0 15.9 - - + -
647A PHE* 3.4 42.3 - - + +
650A VAL* 3.6 29.8 - - + -
651A ASN* 3.7 17.8 + - - +
450B PHE* 4.6 15.4 - - - -
453B ARG* 5.8 0.3 + - - -
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Residues in contact with SER 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A VAL* 1.3 75.8 - - - +
614A ILE* 1.3 70.5 + - - +
616A LYS* 3.8 16.3 + - - -
622A CYS* 3.9 3.8 - - - -
623A PHE* 2.8 35.3 + - - +
625A TYR* 3.6 24.6 + - - -
647A PHE* 4.2 4.3 - - - -
447B GLU 5.0 4.5 + - - -
448B SER* 6.0 0.5 - - - -
450B PHE* 6.4 0.4 - - - -
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Residues in contact with ILE 614 (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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613A SER* 1.3 81.6 + - - +
615A SER* 1.3 77.4 + - - +
616A LYS* 3.3 12.1 + - - +
619A GLU* 4.4 20.2 - - + +
621A CYS 3.6 9.9 - - - +
622A CYS* 4.4 2.2 - - - +
640A GLU* 6.1 0.2 - - - +
643A CYS* 4.0 15.7 - - - -
644A LYS* 3.6 42.0 - - + +
647A PHE* 3.6 35.0 - - + -
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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