Contacts of the helix formed by residues 164 - 174 (chain A) in PDB entry 4D87
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 THR 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A GLU* 4.2 2.0 - - - -
98A ALA* 4.7 4.9 - - + -
161A THR* 6.0 0.4 - - - +
162A LEU 4.9 2.7 - - - +
163A PRO* 1.3 75.9 - - - +
165A ARG* 1.3 54.3 + - - +
166A ASP* 2.5 11.4 + - + -
167A ASP* 2.3 75.4 + - - +
168A VAL* 3.0 3.9 + - - +
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Residues in contact with ARG 165 (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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95A GLU* 2.9 54.0 + - + +
96A THR* 4.9 8.4 - - - +
98A ALA* 5.0 0.6 - - - +
99A GLN* 4.2 23.3 - - - +
164A THR* 1.3 68.9 - - - +
166A ASP* 1.3 66.0 + - + +
167A ASP 3.3 0.2 - - - -
168A VAL* 4.0 5.1 - - - +
169A LEU* 3.8 46.5 + - - +
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Residues in contact with ASP 166 (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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164A THR* 2.5 13.3 + - + -
165A ARG* 1.3 83.0 + - + +
167A ASP* 1.3 61.2 + - - +
169A LEU* 3.9 20.8 - - - +
170A ASN* 3.0 26.8 + - - -
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Residues in contact with ASP 167 (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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163A PRO* 4.4 4.0 - - - +
164A THR* 2.3 60.7 + - - +
166A ASP* 1.3 65.4 - - - +
168A VAL* 1.3 69.2 + - - +
170A ASN* 2.5 32.4 + - - +
171A ALA* 3.2 4.7 + - - -
202A GLN* 3.7 23.0 + - - -
203A LEU* 4.3 15.6 - - + +
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Residues in contact with VAL 168 (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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94A TRP* 4.1 19.7 - - + -
95A GLU* 3.8 35.4 - - + +
164A THR 3.9 4.3 - - - +
165A ARG* 4.0 6.5 - - - +
167A ASP* 1.3 84.3 - - - +
169A LEU* 1.3 69.1 + - + +
171A ALA* 2.9 15.9 + - - +
172A LEU* 3.1 22.0 + - + +
203A LEU* 4.1 11.2 - - + +
237A ILE* 3.6 34.9 - - + +
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Residues in contact with LEU 169 (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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165A ARG* 3.8 37.6 + - - +
166A ASP* 3.9 26.4 + - - +
167A ASP 2.9 2.2 + - - -
168A VAL* 1.3 80.7 - - + +
170A ASN* 1.3 64.6 + - - +
172A LEU* 2.9 30.3 + - + +
173A LYS* 3.3 24.1 + - - +
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Residues in contact with ASN 170 (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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166A ASP* 3.0 22.2 + - - -
167A ASP* 2.5 25.4 + - - +
169A LEU* 1.3 72.6 - - - +
171A ALA* 1.3 55.6 + - - +
173A LYS* 3.0 52.8 + - - +
174A ILE* 3.8 9.6 + - - +
193A GLN* 4.7 7.4 - - - +
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Residues in contact with ALA 171 (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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167A ASP 3.2 2.3 + - - +
168A VAL* 2.9 10.3 + - - +
170A ASN* 1.3 78.8 - - - +
172A LEU* 1.3 58.7 + - + +
173A LYS 3.1 0.2 - - - -
174A ILE* 3.2 21.2 + - - +
190A PHE* 3.2 28.1 - - + -
193A GLN* 4.1 19.6 + - + +
194A LEU* 4.7 6.3 - - + +
203A LEU* 4.0 26.0 - - + -
237A ILE* 6.1 2.5 - - + -
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A VAL* 3.1 25.8 + - + +
169A LEU* 2.9 23.9 + - + +
171A ALA* 1.3 75.8 - - + +
173A LYS* 1.3 54.2 + - - +
174A ILE 3.4 0.2 - - - -
190A PHE* 4.5 0.4 - - + -
237A ILE* 3.6 36.1 - - + +
240A VAL* 3.9 20.2 - - + -
241A TRP* 3.6 31.0 - - + +
244A ILE* 4.0 14.2 - - + +
245A HIS* 2.6 31.5 + - - -
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Residues in contact with LYS 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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169A LEU* 3.6 21.8 - - - +
170A ASN* 3.0 36.7 + - - +
172A LEU* 1.3 78.1 - - + +
174A ILE* 1.3 69.1 + - + +
175A THR* 3.3 7.1 + - - -
245A HIS* 3.7 11.2 - - - -
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Residues in contact with ILE 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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170A ASN 3.9 8.7 - - - +
171A ALA* 3.2 22.0 - - - +
172A LEU 3.4 0.2 - - - -
173A LYS* 1.3 79.8 - - + +
175A THR* 1.3 61.1 + - - +
176A GLN 3.4 4.9 - - - +
188A ASN* 3.2 33.2 - - + +
189A SER 3.5 1.1 - - - -
190A PHE* 3.1 35.7 - - - +
193A GLN* 2.8 35.9 - - - +
241A TRP* 3.1 20.8 + - - -
245A HIS* 3.5 5.9 + - - -
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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