Contacts of the strand formed by residues 500 - 505 (chain B) in PDB entry 1U7V
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 ILE 500 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B GLN 4.5 2.9 - - - +
411B SER* 5.5 1.4 - - - -
412B TYR* 5.4 3.3 + - - -
438B PHE* 6.0 1.2 - - - -
496B ARG* 3.0 48.2 - - + +
497B ARG* 2.9 22.9 + - + +
498B LEU 3.3 2.1 - - - +
499B CYS* 1.3 83.3 - - + +
501B LEU* 1.3 76.6 + - - +
502B ARG* 4.3 7.4 - - + +
526B GLU* 3.8 29.6 - - + +
527B ILE 3.4 2.2 - - - +
528B HIS* 3.0 34.3 - - + +
529B LEU* 4.4 0.2 - - - -
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Residues in contact with LEU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 6.0 0.2 - - + -
397B VAL* 4.4 11.7 - - + -
399B VAL* 5.7 1.6 - - + -
409B VAL* 4.2 10.8 - - + -
410B GLN 3.3 20.6 - - - +
411B SER* 3.6 24.0 - - - +
437B VAL* 3.8 28.3 - - + +
438B PHE* 4.4 12.6 - - + -
500B ILE* 1.3 78.8 - - - +
502B ARG* 1.3 63.1 + - - +
503B MET* 6.0 2.2 - - + -
526B GLU* 3.3 2.4 - - - -
527B ILE* 2.6 63.5 + - + +
529B LEU* 4.0 21.1 - - + -
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Residues in contact with ARG 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B PHE 3.8 0.3 - - - +
409B VAL* 3.5 2.8 - - - +
410B GLN* 2.9 61.6 + - + +
496B ARG* 5.9 1.4 - - - +
497B ARG* 5.7 4.9 - - - +
500B ILE* 4.3 6.5 - - + +
501B LEU* 1.3 78.4 - - - +
503B MET* 1.3 64.0 + - - +
509B TRP* 4.6 0.2 - - - -
518B ILE* 3.2 38.5 - - + +
519B LYS* 4.9 7.5 - - - +
524B TRP* 3.8 19.5 - - + -
525B ILE 3.4 3.1 - - - +
526B GLU* 2.9 35.9 + - + -
317C SER* 5.7 1.2 - - - -
318C ASN 5.8 0.2 - - - -
319C VAL* 4.0 21.8 - - - +
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Residues in contact with MET 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B VAL* 3.8 33.7 - - - -
389B LEU* 4.0 12.1 - - + -
399B VAL* 3.9 26.9 - - + -
407B VAL* 4.6 6.7 - - + -
408B PHE 3.2 11.4 - - - +
409B VAL* 3.4 33.0 - - + -
437B VAL* 5.9 0.4 - - + -
501B LEU* 6.0 2.7 - - + -
502B ARG* 1.3 76.4 - - - +
504B SER* 1.3 65.5 + - - +
505B PHE* 4.1 5.1 + - + -
518B ILE* 4.1 2.3 - - - +
524B TRP* 3.2 4.2 - - - +
525B ILE* 2.8 55.5 + - + +
527B ILE* 4.4 9.4 - - + -
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Residues in contact with SER 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B VAL* 3.5 4.3 - - - +
408B PHE* 2.8 34.7 + - - -
503B MET* 1.3 75.5 - - - +
505B PHE* 1.3 64.4 + - - +
507B LYS 3.0 19.3 + - - -
509B TRP* 3.4 27.2 - - - -
518B ILE* 4.4 0.2 - - - -
521B THR* 3.1 27.4 + - - +
523B CYS 3.7 2.1 + - - -
524B TRP* 3.6 11.2 - - - -
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Residues in contact with PHE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B VAL* 3.5 27.1 - - + -
364B LEU* 3.7 27.6 - - + -
383B ILE* 3.8 24.7 - - + -
386B GLY* 3.8 16.6 - - - -
387B VAL* 3.7 33.0 - - + -
403B SER* 5.7 0.9 - - - -
406B ALA 4.6 1.6 - - - -
407B VAL* 4.1 12.6 - - + -
503B MET* 4.5 8.3 - - + -
504B SER* 1.3 76.0 + - - +
506B VAL* 1.3 69.8 + - + +
507B LYS* 2.9 9.4 + - - +
522B PRO* 4.8 1.0 - - - +
523B CYS* 3.1 37.8 + - - +
524B TRP* 4.5 3.8 - - - -
525B ILE* 4.0 19.5 - - + -
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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