Contacts of the strand formed by residues 31 - 35 (chain D) in PDB entry 6D6Q
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 PHE 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D LEU* 4.3 23.1 - - + -
29D ARG 3.1 20.2 - - - +
30D HIS* 1.3 80.2 + - - +
32D ALA* 1.3 58.7 + - - +
47D PHE* 3.9 23.8 - + + -
48D LEU* 3.5 6.1 - - - +
49D GLN* 3.2 33.7 - - + -
168D ASP* 5.6 0.2 - - - -
219D HIS* 4.8 4.3 - - + -
220D VAL* 4.2 29.6 - - + -
223D PHE* 3.4 55.4 - + + -
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Residues in contact with ALA 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D HIS* 4.9 13.4 - - + +
31D PHE* 1.3 74.7 - - - +
33D CYS* 1.3 66.5 + - - +
47D PHE* 3.8 5.0 - - - -
48D LEU* 2.8 45.1 + - + +
223D PHE* 3.7 11.0 - - + -
230D ARG* 5.4 4.7 - - - +
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Residues in contact with CYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ALA* 1.3 79.5 - - - +
34D GLU* 1.3 76.5 + - - +
35D GLN* 3.2 26.9 - - - -
45D ALA* 4.4 1.1 - - - -
46D SER 3.1 19.5 - - - -
47D PHE* 3.8 15.5 - - + -
48D LEU* 6.0 0.2 - - - -
139D MET* 4.0 21.8 - - + -
223D PHE* 4.2 15.8 - - + -
224D TYR* 6.5 0.4 - - + -
227D SER* 5.0 10.7 + - - +
230D ARG* 4.1 15.4 + - - -
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Residues in contact with GLU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D CYS* 1.3 80.8 - - - +
35D GLN* 1.3 73.7 + - - +
36D ASN 5.4 0.7 - - - +
37D LEU* 3.2 35.9 - - + +
45D ALA* 3.3 5.7 - - - -
46D SER* 2.9 35.6 + - - +
227D SER* 5.9 0.7 - - - -
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Residues in contact with GLN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D CYS* 3.2 20.1 - - - -
34D GLU* 1.3 87.0 - - - +
36D ASN* 1.3 77.0 + - - +
37D LEU 3.4 2.2 + - - -
44D SER 3.6 2.9 + - - -
45D ALA* 3.1 24.1 - - - +
139D MET* 2.8 40.8 + - - +
142D VAL* 4.9 1.6 - - - +
143D ASP* 3.4 26.2 + - - +
227D SER* 5.1 8.3 - - - +
228D LEU* 4.9 16.7 - - + +
231D ARG* 4.8 15.7 - - + +
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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