Contacts of the strand formed by residues 2 - 6 (chain X) in PDB entry 1KD1
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 HIS 2 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET* 1.3 77.5 - - - +
3X ALA* 1.3 60.9 + - - +
34X LEU* 3.4 3.5 - - - -
35X VAL* 2.8 49.9 + - + +
37X GLU* 3.4 39.6 + - + +
45X VAL* 5.9 6.3 - - + +
54X PHE* 4.3 22.9 - + + -
55X GLY* 3.3 15.7 - - - +
56X GLU* 3.2 30.9 + - - +
140X LYS* 4.5 20.3 + - - -
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Residues in contact with ALA 3 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X HIS* 1.3 73.7 - - - +
4X LEU* 1.3 61.1 + - - +
5X VAL* 4.8 0.6 - - - +
32X CYS* 4.6 6.7 - - - -
33X THR 3.6 5.4 - - - +
34X LEU* 4.3 12.8 - - + -
53X ALA 3.4 2.1 - - - +
54X PHE* 3.1 24.1 - - - -
55X GLY 2.7 16.0 + - - +
57X PRO* 4.1 12.0 - - + +
146X ILE* 4.2 5.3 - - + +
150X LEU* 4.0 29.2 - - + -
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Residues in contact with LEU 4 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X HIS 3.8 0.8 + - - -
3X ALA* 1.3 72.1 - - - +
5X VAL* 1.3 62.0 + - - +
6X GLN 4.3 0.4 - - - -
21X LEU* 4.6 10.5 - - + -
24X LEU* 3.7 31.6 - - + -
26X ILE* 5.0 4.6 - - + +
31X HIS 3.7 0.9 - - - +
32X CYS* 2.8 27.2 - - - +
33X THR* 2.7 37.0 + - + +
35X VAL* 4.5 12.3 - - + -
45X VAL* 4.9 11.0 - - + -
48X VAL* 4.6 4.3 - - + -
52X VAL* 3.0 46.9 - - + -
53X ALA 3.6 0.2 - - - +
54X PHE* 3.5 19.3 - - + -
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Residues in contact with VAL 5 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X ALA 4.8 2.5 - - - +
4X LEU* 1.3 80.1 - - - +
6X GLN* 1.3 73.1 + - - +
7X LEU* 3.4 10.3 + - + +
30X ASN* 4.3 11.7 - - - +
31X HIS 3.5 7.2 - - - +
32X CYS* 3.6 16.6 - - + -
52X VAL* 2.8 16.9 - - - +
53X ALA* 2.9 35.9 + - + +
118X LEU* 4.1 1.8 - - + -
146X ILE* 5.4 1.6 - - + -
149X LEU* 4.9 3.4 - - + -
150X LEU* 3.9 24.0 - - + -
153X MET* 3.6 25.6 - - + -
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Residues in contact with GLN 6 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X VAL* 1.3 70.6 - - - +
7X LEU* 1.3 61.5 + - - +
8X ARG 2.6 28.5 + - - +
9X GLY* 4.1 11.5 + - - -
10X GLU* 4.5 3.2 - - - +
13X MET* 4.5 4.8 - - - -
18X GLN* 6.2 0.8 - - - +
21X LEU* 3.5 23.1 - - + +
26X ILE* 3.3 30.9 - - + +
27X HIS 4.4 1.4 - - - -
28X HIS* 3.2 31.8 + - - +
29X VAL* 3.7 10.3 - - - -
30X ASN* 2.8 31.2 + - - -
31X HIS 3.1 9.8 + - - +
51X PHE 3.7 4.0 + - - +
52X VAL* 3.6 9.9 - - + +
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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