Contacts of the helix formed by residues 158 - 163 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76S ASN* 3.3 13.9 + - - +
81S TYR* 3.9 18.8 - + - +
40T GLN* 5.7 0.2 + - - -
43T LEU* 3.3 29.3 - - + +
79T PHE* 4.1 20.6 - + + -
113T VAL* 4.0 21.8 - - + -
115T LEU* 3.3 47.6 - - + -
119T SER* 4.6 4.5 - - - -
120T TYR* 4.8 5.8 - - - -
121T HIS* 3.5 31.2 - + - -
154T ALA 4.7 0.2 - - - -
155T LEU* 3.0 45.1 + - + +
156T ARG 3.0 0.6 + - - -
157T SER* 1.3 79.6 - - - +
159T GLY* 1.3 55.7 + - - +
162T LEU* 4.7 3.1 - - + -
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Residues in contact with GLY 159 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73S ASN* 4.3 4.5 - - - -
76S ASN* 3.6 10.5 - - - +
43T LEU* 3.7 8.5 - - - -
156T ARG 3.1 8.3 + - - +
157T SER 3.3 1.2 - - - -
158T PHE* 1.3 81.4 - - - +
160T ASN* 1.3 66.8 + - - -
161T ALA* 3.3 2.9 - - - -
162T LEU* 3.1 12.8 + - - +
163T GLY 3.5 0.7 + - - -
164T ASN* 3.1 21.6 + - - +
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Residues in contact with ASN 160 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69S HIS* 6.1 0.3 - - - -
73S ASN* 3.1 31.9 + - - +
43T LEU 3.1 4.2 + - - +
44T ARG* 2.9 25.2 + - - +
45T GLN 3.1 17.0 - - - +
46T ARG* 4.2 16.8 + - - +
47T LEU* 3.0 12.5 - - - +
159T GLY* 1.3 71.4 - - - -
161T ALA* 1.3 55.5 + - - +
163T GLY 2.8 22.9 + - - -
164T ASN* 3.5 10.0 + - - +
165T CYS* 3.6 29.5 + - + +
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Residues in contact with ALA 161 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192S LYS* 4.6 11.6 - - + +
42T ALA 3.4 25.6 - - - +
43T LEU* 2.8 17.4 + - + +
45T GLN* 2.9 12.3 + - + +
47T LEU* 3.7 10.8 - - - +
74T LEU* 3.5 25.3 - - - +
78T MET* 3.8 16.8 - - + -
159T GLY 3.3 0.2 - - - -
160T ASN* 1.3 74.9 - - - +
162T LEU* 1.3 60.7 + - - +
163T GLY 3.4 0.9 - - - -
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Residues in contact with LEU 162 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43T LEU* 3.7 23.6 - - + -
66T ILE* 5.0 4.0 - - - +
71T VAL* 4.3 14.1 - - + +
74T LEU* 4.2 15.7 - - + -
75T ALA* 4.0 25.4 - - + +
78T MET* 4.1 23.3 - - + -
79T PHE* 4.5 8.7 - - + -
152T LYS 4.8 1.0 - - - +
155T LEU* 3.5 46.7 - - + +
156T ARG* 3.9 13.7 + - - +
158T PHE* 4.7 5.4 - - + -
159T GLY* 3.1 9.5 + - - +
160T ASN 3.0 0.8 - - - -
161T ALA* 1.3 84.3 - - - +
163T GLY* 1.3 57.5 + - - +
164T ASN 3.8 0.7 - - - -
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Residues in contact with GLY 163 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T LEU* 4.3 3.2 - - - +
66T ILE* 3.9 23.1 - - - +
156T ARG* 3.7 14.0 + - - -
160T ASN 2.8 9.0 + - - -
161T ALA 3.4 1.4 + - - -
162T LEU* 1.3 81.5 - - - +
164T ASN* 1.3 63.5 + - - +
165T CYS* 3.1 5.0 + - - -
166T ILE* 3.2 25.6 - - - +
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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