Contacts of the strand formed by residues 1604 - 1607 (chain F) in PDB entry 6X34
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 SER1604 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1111F PRO* 4.7 4.6 - - - +
1239F SER* 3.5 8.0 - - - -
1240F LYS* 2.9 32.5 + - - -
1244F GLN* 3.3 41.5 + - - -
1601F MET* 5.5 3.6 - - - -
1603F VAL* 1.3 75.7 - - - +
1605F TRP* 1.3 82.9 + - - +
1656F ARG* 5.7 0.5 + - - -
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Residues in contact with TRP1605 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074F ILE* 4.6 13.9 - - + -
1076F ARG* 3.6 30.1 - - + -
1077F ALA 5.6 1.1 - - - -
1107F PRO 6.1 0.7 - - - -
1109F LEU* 3.7 43.2 + - + -
1111F PRO* 3.5 37.0 - - + +
1237F TRP* 4.7 28.7 - + + -
1238F PHE 4.3 7.4 - - - -
1239F SER* 5.0 2.7 - - - -
1240F LYS* 4.5 1.4 - - - +
1244F GLN* 5.0 2.8 + - - -
1604F SER* 1.3 94.8 + - - +
1606F SER* 1.3 63.7 + - - +
1656F ARG* 4.1 17.0 + - - +
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Residues in contact with SER1606 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237F TRP* 3.4 12.6 - - - -
1238F PHE* 3.1 50.8 + - - +
1240F LYS* 3.7 22.0 - - - -
1605F TRP* 1.3 76.4 - - - +
1607F ARG* 1.3 62.8 + - - +
1656F ARG* 5.4 2.2 - - - +
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Residues in contact with ARG1607 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696F PRO 5.7 0.2 - - - +
1236F THR 4.3 1.8 - - - +
1237F TRP* 3.6 27.8 - - + -
1238F PHE* 3.3 13.5 - - - -
1606F SER* 1.3 75.9 - - - +
1608F MET* 1.3 63.5 + - - +
1609F PRO* 3.9 6.2 - - - +
1649F ASP* 5.5 6.9 - - + +
1652F GLU* 3.7 31.2 - - + +
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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