Contacts of the strand formed by residues 4029 - 4034 (chain B) in PDB entry 4O2W
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 ALA4029 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3996B LYS* 5.7 1.4 - - - +
3997B CYS* 3.5 20.2 - - - +
3999B VAL* 4.4 4.3 - - + -
4026B PHE 2.9 18.0 + - - +
4027B SER 3.3 1.3 - - - +
4028B GLN* 1.3 79.8 - - - +
4030B GLN* 1.3 59.9 + - - +
4031B GLN 3.9 2.5 - - - +
4032B VAL* 3.8 25.6 - - + -
4041B VAL* 3.5 30.4 - - + +
4042B ILE 3.9 0.2 - - - -
4358B TRP* 5.2 0.2 - - + -
4360B ALA* 3.6 5.2 - - - +
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Residues in contact with GLN4030 (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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4028B GLN 3.6 1.6 + - - -
4029B ALA* 1.3 73.4 - - - +
4031B GLN* 1.3 72.5 + - + +
4042B ILE* 2.8 14.1 + - + +
4043B GLN 4.0 2.0 - - - +
4044B ALA* 3.8 30.4 - - + +
4347B GLN* 3.2 21.6 + - - +
4358B TRP* 2.9 18.2 + - - -
4360B ALA* 3.3 31.3 + - - +
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Residues in contact with GLN4031 (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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4029B ALA* 3.9 0.4 - - - +
4030B GLN* 1.3 94.6 - - + +
4032B VAL* 1.3 67.4 + - - +
4033B ILE* 4.2 9.3 - - + +
4041B VAL* 3.3 6.8 - - - +
4042B ILE* 3.0 49.7 + - + +
4082B THR* 2.8 28.1 + - - +
4083B GLN* 3.4 5.1 + - - +
4347B GLN* 4.4 11.1 - - - +
4358B TRP* 3.8 7.2 - - + +
4405B UNX 2.7 26.8 + - - -
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Residues in contact with VAL4032 (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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3999B VAL* 4.2 13.9 - - + -
4001B LEU* 4.5 2.0 - - + -
4026B PHE* 4.2 13.7 - - + -
4029B ALA* 3.8 19.1 - - + -
4031B GLN* 1.3 78.5 - - - +
4033B ILE* 1.3 66.4 + - - +
4034B CYS* 4.1 0.7 - - - -
4039B THR* 3.7 25.4 - - + -
4040B PHE 3.4 4.5 - - - +
4041B VAL* 4.5 0.7 - - + -
4349B SER* 3.4 7.8 - - - -
4356B ALA* 3.9 20.0 - - + -
4358B TRP* 3.1 52.0 - - + -
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Residues in contact with ILE4033 (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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4031B GLN* 4.2 10.1 - - + +
4032B VAL* 1.3 81.9 - - - +
4034B CYS* 1.3 66.2 + - - +
4035B GLY 3.9 0.9 + - - -
4039B THR* 3.5 3.0 - - - -
4040B PHE* 2.8 53.6 + - + +
4042B ILE* 4.1 31.9 - - + -
4084B LEU* 3.5 39.7 - - + +
4085B VAL* 4.5 0.9 - - - -
4086B THR* 3.9 25.6 - - + +
4349B SER* 3.7 4.3 - - - +
4405B UNX 4.6 6.1 - - - +
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Residues in contact with CYS4034 (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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4001B LEU* 5.2 0.7 - - - -
4032B VAL* 4.7 0.2 - - - -
4033B ILE* 1.3 76.2 - - - +
4035B GLY* 1.3 57.9 + - - +
4038B CYS 3.8 4.3 - - - -
4039B THR* 4.4 8.3 - - - +
4086B THR* 3.9 6.9 - - - +
4088B CYS* 4.4 3.8 - - - -
4349B SER* 2.9 17.7 + - - +
4350B ALA 3.5 6.4 - - - +
4351B GLY* 3.5 29.9 - - - +
4354B HIS* 3.6 28.0 - - + +
4355B SER 3.9 1.8 - - - -
4356B ALA* 3.5 40.4 - - - -
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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