Contacts of the strand formed by residues 374 - 379 (chain A) in PDB entry 5W5G
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 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A LYS* 4.9 5.2 - - - -
373A ARG* 1.3 78.9 - - - +
375A LEU* 1.3 60.1 + - - +
376A PHE* 3.5 31.0 - - + -
558A ASN 3.5 3.8 + - - +
559A ASN* 3.1 22.1 + - - +
560A ILE* 3.2 24.5 + - - +
601A SER* 4.8 2.9 - - - -
602A CYS 3.2 8.1 - - - +
603A GLU* 4.2 24.0 - - - -
611A TRP* 4.2 3.9 - - - -
614A THR* 5.4 1.6 - - - -
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Residues in contact with LEU 375 (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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374A CYS* 1.3 72.2 - - - +
376A PHE* 1.3 65.9 + - - +
377A VAL* 4.2 16.1 + - + +
546A THR* 3.8 27.1 - - + -
549A ILE* 5.4 0.9 - - + -
550A ILE* 4.3 8.5 - - + -
560A ILE* 3.6 28.7 - - + +
562A ILE* 3.7 24.7 - - + -
572A CYS 5.8 0.2 - - - -
573A THR* 5.0 4.9 - - + -
576A LEU* 3.8 19.3 - - + -
601A SER* 3.4 3.1 - - - -
602A CYS* 2.7 47.7 + - + +
611A TRP* 4.0 13.6 - - + -
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Residues in contact with PHE 376 (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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374A CYS* 3.5 26.2 - - + -
375A LEU* 1.3 74.5 - - - +
377A VAL* 1.3 59.1 + - - +
445A LEU* 5.4 0.2 - - + -
450A THR* 3.7 22.0 - - + -
452A ILE* 3.6 32.8 - - + -
559A ASN* 4.0 14.6 - - - -
560A ILE 2.8 19.3 + - - +
561A LEU* 3.4 8.4 - - + -
562A ILE* 2.7 32.9 + - - +
599A PHE* 3.7 30.1 - + + -
600A CYS 3.7 1.6 - - - -
601A SER* 3.2 32.5 - - - -
617A PRO* 3.9 20.9 - - + -
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Residues in contact with VAL 377 (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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375A LEU* 4.2 11.4 - - + +
376A PHE* 1.3 78.2 - - - +
378A CYS* 1.3 65.5 + - - +
562A ILE* 3.4 32.8 - - + +
564A ALA 5.7 0.7 - - - +
568A SER* 4.1 9.2 - - - +
569A LEU* 3.7 34.9 - - + +
572A CYS* 4.7 6.5 - - + -
573A THR* 4.2 19.7 - - + -
598A GLY 3.9 0.5 - - - +
599A PHE* 3.6 0.4 - - - -
600A CYS* 2.9 44.9 + - - +
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Residues in contact with CYS 378 (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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376A PHE 4.3 0.2 - - - -
377A VAL* 1.3 76.7 - - - +
379A ARG* 1.3 68.2 + - - +
470A ILE* 3.8 29.6 - - - -
561A LEU* 4.3 7.4 - - - -
562A ILE 3.0 7.3 + - - -
563A VAL* 3.4 14.4 - - - -
564A ALA 3.0 24.6 + - - -
569A LEU* 4.0 6.3 - - - -
597A LEU* 4.1 7.9 - - - +
598A GLY 3.1 13.7 - - - +
599A PHE* 3.6 23.3 - - + -
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Residues in contact with ARG 379 (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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378A CYS* 1.3 75.8 - - - +
380A HIS* 1.3 90.4 + - + +
383A ARG* 5.4 3.4 - - - +
563A VAL* 4.8 0.4 - - - -
564A ALA 3.4 6.3 - - - -
565A HIS 4.1 0.9 - - - -
566A ALA* 3.8 33.9 - - - +
569A LEU* 3.8 12.7 - - + +
591A VAL 5.9 0.2 - - - -
594A ILE* 2.7 33.7 + - + -
595A PRO* 3.5 21.7 - - - +
596A TYR* 3.3 46.1 + - - +
597A LEU* 3.3 24.0 - - - +
598A GLY 3.1 9.4 + - - +
626B THR 4.7 2.0 + - - -
627B GLY* 5.4 1.2 + - - -
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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