Contacts of the helix formed by residues 172 - 180 (chain A) in PDB entry 1X1O
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 LYS 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ARG* 4.6 13.0 - - - +
162A ARG* 4.4 14.3 - - - +
165A LEU* 6.1 0.7 - - + -
170A LEU* 3.6 23.9 - - + +
171A LEU* 1.3 76.4 - - - +
173A GLU* 1.3 68.7 + - - +
174A ASN* 3.1 7.0 - - + +
175A HIS* 2.9 31.3 + - + +
176A VAL* 3.0 14.0 + - - +
202A GLU* 2.7 38.3 + - - +
104B GLU* 5.2 11.2 - - - +
105B ARG* 6.2 3.8 - - - +
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LYS* 1.3 74.6 - - - +
174A ASN* 1.3 58.0 + - - +
176A VAL* 3.2 11.0 + - + +
177A ARG* 2.9 52.6 + - + +
202A GLU* 3.3 15.3 + - + +
204A ARG* 3.6 48.1 + - - +
223A ASP* 4.6 6.8 - - - +
282B LEU* 3.8 22.3 - - + +
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Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LYS* 3.1 5.1 - - + +
173A GLU* 1.3 78.5 - - - +
175A HIS* 1.3 59.8 + - + +
177A ARG* 3.5 4.8 + - - +
178A ALA* 3.0 27.9 + - - +
101B LEU* 3.6 20.5 - - + +
104B GLU* 3.0 27.3 + - - -
281B LEU* 3.0 26.0 + - - +
282B LEU* 3.5 13.5 - - - +
283B VAL* 2.9 37.6 + - + +
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Residues in contact with HIS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ARG* 6.1 0.4 - - - -
165A LEU* 6.1 4.3 - - + -
170A LEU 3.7 7.5 + - - -
171A LEU* 4.0 15.9 - - + -
172A LYS* 2.9 40.9 + - + +
174A ASN* 1.3 74.7 - - + +
176A VAL* 1.3 61.1 + - - +
178A ALA* 3.2 5.9 + - - +
179A ALA* 2.9 32.8 + - - +
185A ALA* 4.7 1.6 - - - -
30B ASP* 4.8 1.5 + - - -
32B THR* 3.6 30.5 - - + +
33B SER* 2.9 35.0 + - - -
36B VAL* 4.0 11.9 - - + +
37B VAL* 4.6 0.4 - - + -
101B LEU* 4.0 20.4 - - + +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU 4.6 1.3 - - - +
172A LYS 3.0 17.8 + - - +
173A GLU* 3.5 11.7 - - + +
175A HIS* 1.3 77.1 - - - +
177A ARG* 1.3 62.8 + - + +
180A GLY 3.0 4.0 + - - -
181A GLY* 2.9 55.0 + - - +
182A VAL* 3.6 28.0 - - + +
185A ALA* 4.3 6.7 - - + -
201A VAL* 4.2 13.0 - - + -
202A GLU 4.1 14.6 - - - +
208A GLU* 5.4 4.9 - - - +
285B ARG* 5.2 2.4 + - - +
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLU* 2.9 39.0 + - + +
174A ASN* 3.8 8.1 - - - +
176A VAL* 1.3 79.5 - - + +
178A ALA* 1.3 61.1 + - - +
180A GLY* 3.4 11.3 + - - -
282B LEU* 3.3 43.5 - - - +
283B VAL* 2.7 36.8 + - + +
284B VAL* 4.4 1.8 - - - +
285B ARG* 3.3 72.6 + - + +
286B PRO* 3.4 17.7 - - - +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ASN 3.0 19.5 + - - +
175A HIS* 3.2 5.4 + - - +
177A ARG* 1.3 79.9 - - - +
179A ALA* 1.3 58.4 + - - +
180A GLY 3.7 0.3 + - - -
188A ARG* 4.8 4.5 + - - -
36B VAL 5.0 3.2 - - - +
37B VAL* 4.2 20.2 - - + -
38B PRO* 5.9 0.2 - - - +
41B LEU* 4.6 9.5 - - + +
97B LEU* 3.9 24.9 - - + -
101B LEU* 5.2 2.0 - - + -
283B VAL* 4.9 3.1 - - + +
286B PRO* 4.2 19.8 - - - +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A HIS 2.9 17.0 + - - +
176A VAL 4.2 1.1 - - - +
178A ALA* 1.3 75.3 - - - +
180A GLY* 1.3 61.9 + - - +
181A GLY 4.4 0.2 - - - +
184A GLU* 3.5 14.4 - - - +
185A ALA* 3.7 32.1 - - + +
188A ARG* 3.8 35.1 + - - +
36B VAL* 4.5 9.4 - - + -
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Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A VAL 3.0 4.7 + - - -
177A ARG* 3.4 8.3 + - - -
178A ALA 3.4 3.8 + - - -
179A ALA* 1.3 79.2 - - - +
181A GLY* 1.3 57.0 + - - +
184A GLU* 3.7 14.0 - - - +
285B ARG* 5.8 5.2 - - - -
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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