Contacts of the strand formed by residues 10 - 13 (chain M) in PDB entry 1K6L
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 VAL 10 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H VAL* 3.7 28.9 - - + -
144H ALA 3.9 5.2 - - - -
145H GLY* 4.9 0.7 - - - -
146H LYS 3.3 20.6 - - - +
148H PRO* 4.1 15.3 - - + -
167H ILE* 4.6 6.7 - - + -
176H ALA* 4.3 17.6 + - + +
193H MET* 4.2 14.3 - - + +
198H VAL* 4.1 18.8 - - + -
8M SER* 3.4 10.3 - - - -
9M GLN* 1.3 89.8 - - - +
11M GLN* 1.3 69.6 + - - +
12M VAL* 4.0 5.3 + - + -
41M TRP* 4.8 0.8 - - - -
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Residues in contact with GLN 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H VAL* 3.1 12.5 - - - +
143H SER* 2.8 42.4 + - - +
144H ALA* 3.0 19.8 + - + -
8M SER* 5.0 2.7 - - - -
10M VAL* 1.3 75.4 - - - +
12M VAL* 1.3 60.6 + - - +
13M ARG* 5.0 1.2 + - - -
37M THR* 2.7 53.6 + - - +
40M GLY* 3.2 32.9 - - - +
41M TRP* 3.4 16.4 - - + +
45M ALA* 4.1 10.2 - - - +
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Residues in contact with VAL 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H MET* 4.4 9.6 - - - -
140H PHE* 3.2 34.5 - - + -
141H HIS 3.3 9.0 - - - +
142H VAL* 4.6 8.5 - - + -
143H SER* 4.1 1.5 + - - -
167H ILE* 4.4 11.7 - - + -
169H VAL* 3.6 28.0 - - + -
174H GLN* 3.5 22.2 + - - +
175H MET* 4.8 5.6 - - - +
176H ALA* 4.5 20.3 - - + +
10M VAL* 4.0 3.7 + - + -
11M GLN* 1.3 81.1 - - - +
13M ARG* 1.3 60.4 + - - +
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Residues in contact with ARG 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H PHE* 2.9 30.1 - - - -
141H HIS* 2.9 39.3 + - + +
143H SER* 4.0 26.3 + - - +
174H GLN* 3.5 5.2 - - - +
11M GLN* 5.0 2.8 + - - -
12M VAL* 1.3 75.6 - - - +
14M GLY* 1.3 79.2 + - - +
35M PHE* 3.4 57.8 + - + +
37M THR* 3.4 25.5 + - - +
45M ALA* 5.0 3.8 - - - +
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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