Contacts of the helix formed by residues 158 - 163 (chain K) in PDB entry 1H2I
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 158 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76J ASN* 3.3 14.8 + - - +
81J TYR* 3.9 21.1 - + + +
43K LEU* 3.3 30.2 - - + +
79K PHE* 4.1 20.0 - + + -
113K VAL* 4.0 16.6 - - + -
115K LEU* 3.2 46.4 - - + -
119K SER* 4.6 3.6 - - - -
120K TYR* 4.8 12.1 - - - -
121K HIS* 3.6 27.1 - + - -
154K ALA 4.8 0.2 - - - -
155K LEU* 3.1 42.1 + - + +
156K ARG 2.9 1.8 + - - -
157K SER* 1.3 78.2 - - - +
159K GLY* 1.3 56.1 + - - +
162K LEU* 4.7 4.0 - - + -
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Residues in contact with GLY 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J ASN* 4.4 4.9 - - - -
76J ASN* 3.9 9.2 - - - -
43K LEU* 4.0 7.6 - - - -
155K LEU 4.3 0.2 + - - -
156K ARG 2.9 8.3 + - - +
157K SER 3.3 1.2 + - - -
158K PHE* 1.3 82.0 - - - +
160K ASN* 1.3 67.5 + - - -
161K ALA 3.3 2.5 - - - -
162K LEU* 3.1 10.2 + - - +
163K GLY 3.5 0.5 + - - -
164K ASN* 3.0 23.9 + - - +
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Residues in contact with ASN 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J HIS* 6.1 0.3 - - - -
73J ASN* 3.2 33.0 + - - +
43K LEU 3.1 4.0 + - - -
44K ARG* 2.7 25.3 + - - +
45K GLN 3.1 17.0 - - - +
46K ARG* 4.2 22.0 + - - +
47K LEU* 3.0 12.7 - - - +
159K GLY* 1.3 71.2 - - - -
161K ALA* 1.3 57.0 + - - +
163K GLY* 2.7 25.1 + - - -
164K ASN* 3.4 9.5 + - - +
165K CYS* 3.7 22.8 + - + +
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Residues in contact with ALA 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192J LYS* 4.6 10.3 - - - -
42K ALA 3.4 25.6 - - - +
43K LEU* 2.8 20.8 + - + +
45K GLN* 2.9 13.6 + - + +
47K LEU* 3.7 11.5 - - - +
74K LEU* 3.6 26.9 - - - +
78K MET* 3.8 16.8 - - + -
159K GLY 3.3 0.4 - - - -
160K ASN* 1.3 70.7 - - - +
162K LEU* 1.3 59.4 + - - +
163K GLY 3.3 0.7 - - - -
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Residues in contact with LEU 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K LEU* 3.7 23.8 - - + -
66K ILE* 5.1 1.8 - - - +
71K VAL* 4.2 14.2 - - + +
74K LEU* 4.0 16.8 - - + -
75K ALA* 3.9 23.8 - - + +
78K MET* 4.1 23.3 - - + -
79K PHE* 4.6 9.6 - - + -
152K LYS 4.7 1.6 - - - +
155K LEU* 3.5 45.6 - - + +
156K ARG* 3.8 14.9 + - - +
158K PHE* 4.7 6.1 - - + -
159K GLY 3.1 9.3 + - - +
160K ASN 2.8 1.0 + - - -
161K ALA* 1.3 83.1 - - - +
163K GLY* 1.3 56.9 - - - +
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Residues in contact with GLY 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K LEU* 4.3 4.7 - - - +
66K ILE* 3.8 23.8 - - - +
156K ARG* 3.7 14.3 - - - -
160K ASN 2.7 9.4 + - - -
161K ALA 3.3 1.4 - - - -
162K LEU* 1.3 79.6 - - - +
164K ASN* 1.3 62.0 + - - +
165K CYS 3.1 4.4 + - - -
166K ILE* 3.2 24.9 + - - +
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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