Contacts of the strand formed by residues 621 - 626 (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 CYS 621 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A ILE* 3.6 2.4 - - - +
615A SER* 3.0 27.8 + - - -
618A GLU* 2.8 14.2 + - + +
619A GLU 3.2 0.2 - - - -
620A ARG* 1.3 78.9 - - - +
622A CYS* 1.3 67.3 + - - +
623A PHE* 4.0 22.0 - - - -
634A GLN* 4.1 5.6 - - - -
635A ILE 3.1 16.8 - - - -
636A TYR* 3.5 43.3 - - + +
643A CYS* 3.4 9.8 - - - -
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Residues in contact with CYS 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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612A VAL* 3.8 18.8 - - - -
613A SER 3.6 14.6 - - - -
614A ILE* 4.2 3.1 - - - -
621A CYS* 1.3 75.9 - - - +
623A PHE* 1.3 73.6 + - - +
633A PHE 3.6 0.5 - - - +
635A ILE* 2.6 45.8 + - - +
637A PHE* 4.0 4.0 - - + -
643A CYS* 3.7 15.8 - - - +
646A PHE* 4.0 27.8 - - + -
647A PHE* 4.2 13.2 - - - -
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Residues in contact with PHE 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A VAL* 3.2 6.9 - - - +
613A SER* 2.8 37.5 + - - +
614A ILE 4.9 0.2 - - - -
615A SER* 4.0 28.3 - - - -
621A CYS* 4.0 11.4 - - - -
622A CYS* 1.3 80.4 - - - +
624A LEU* 1.3 59.4 + - - +
625A TYR* 3.2 32.1 - + + +
632A ASP* 4.2 18.4 - - + -
633A PHE 3.3 5.2 - - - -
634A GLN* 3.4 43.5 - - + +
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Residues in contact with LEU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ILE* 4.2 23.3 - - + -
588A ILE* 3.8 28.9 - - + -
604A PHE* 4.5 3.4 - - + -
609A VAL* 3.6 30.3 - - + -
611A GLY 3.7 7.4 - - - +
612A VAL* 3.9 14.1 - - + -
622A CYS 3.9 0.2 + - - -
623A PHE* 1.3 73.2 - - - +
625A TYR* 1.3 62.4 + - - +
626A VAL* 4.1 17.9 + - + -
632A ASP* 3.7 5.2 - - - +
633A PHE* 2.9 39.1 + - + +
635A ILE* 3.9 20.9 - - + -
646A PHE* 4.6 5.2 - - + -
650A VAL* 4.4 0.2 - - + -
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Residues in contact with TYR 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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609A VAL* 3.7 2.9 - - - +
610A ARG* 2.8 72.7 + - + +
611A GLY* 2.9 29.8 + - - +
612A VAL 4.1 0.9 - - - -
613A SER* 3.6 28.8 + - - -
623A PHE* 3.2 37.0 - + + +
624A LEU* 1.3 73.8 - - - +
626A VAL* 1.3 59.4 + - - +
632A ASP* 3.3 40.8 - - - +
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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
----------------------------------------------------------
604A PHE* 3.6 55.2 - - + -
608A SER* 3.4 11.4 - - - +
609A VAL* 4.6 4.0 - - + -
610A ARG* 4.2 4.9 + - - +
624A LEU* 4.1 18.5 + - + -
625A TYR* 1.3 80.3 - - - +
627A LEU* 1.3 67.8 + - - +
629A ASN* 3.4 41.0 + - + +
631A ASP 5.4 2.3 + - - +
632A ASP* 5.8 0.2 - - - +
633A PHE* 3.9 10.8 - - + -
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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