Contacts of the helix formed by residues 59 - 63 (chain B) in PDB entry 3KDH
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 ASN 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B LEU 4.7 6.0 - - - +
56B ARG* 3.0 25.6 + - + +
58B ASP* 1.3 88.8 + - - +
60B PRO* 1.3 64.9 - - - +
61B GLU* 3.1 27.1 + - - +
62B ARG* 2.8 49.7 + - - +
63B TYR* 4.7 0.3 + - - -
187B HIS* 3.7 11.8 + - - -
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Residues in contact with PRO 60 (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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53B LEU 5.6 0.2 - - - +
56B ARG 4.3 1.3 - - - +
57B PHE 3.6 7.4 - - - +
58B ASP 3.4 6.5 - - - -
59B ASN* 1.3 91.2 - - - +
61B GLU* 1.3 70.2 + - + +
63B TYR* 3.1 15.5 + - + -
64B LYS* 3.0 49.3 + - + +
67B VAL* 5.0 5.8 - - + -
70B CYS* 3.4 24.5 - - + -
83B ARG* 4.0 19.7 - - - +
85B VAL* 4.6 8.1 - - + -
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Residues in contact with GLU 61 (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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58B ASP 3.7 1.1 - - - +
59B ASN* 3.1 26.7 + - - +
60B PRO* 1.3 85.2 - - - +
62B ARG* 1.3 58.5 + - - +
63B TYR 3.1 0.2 - - - -
64B LYS 3.9 7.9 - - - -
67B VAL* 3.2 36.1 - - + +
68B LYS 5.5 0.4 - - - -
69B ARG* 4.8 3.1 - - - -
70B CYS* 3.5 24.8 + - - +
176B LYS* 2.9 28.2 + - - -
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Residues in contact with ARG 62 (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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53B LEU* 3.3 37.7 - - + +
56B ARG* 6.5 0.4 - - - -
59B ASN* 2.8 40.8 + - - +
60B PRO 3.0 1.0 - - - -
61B GLU* 1.3 79.5 - - + +
63B TYR* 1.3 62.5 + - + +
176B LYS* 3.5 11.2 - - - +
180B ALA* 4.1 21.5 + - - +
184B ALA* 4.5 12.9 + - - +
185B PRO 3.0 27.1 + - - -
186B MET* 4.3 3.4 - - - +
187B HIS* 3.1 53.8 + - - +
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Residues in contact with TYR 63 (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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53B LEU* 3.9 26.7 - - + -
54B ILE* 4.2 26.9 + - + +
59B ASN 5.1 0.9 - - - -
60B PRO* 3.1 16.6 + - + -
62B ARG* 1.3 83.3 - - - +
64B LYS* 1.3 90.3 + - + +
112B PHE* 5.6 1.7 - - - -
128B THR* 5.0 4.4 + - + +
147B GLU* 4.8 9.2 + - - -
173B ASN* 2.9 30.8 - - + +
174B LEU* 4.6 10.5 - - + -
176B LYS* 3.4 17.7 - - - +
177B LEU* 3.5 52.0 - - + -
180B ALA* 5.4 1.1 - - + -
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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