Contacts of the helix formed by residues 165 - 178 (chain A) in PDB entry 2FD5
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 GLY 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ARG* 4.6 1.8 - - - +
163A GLY 3.4 1.9 + - - -
164A PRO* 1.3 75.1 - - - +
166A GLU* 1.3 60.9 + - - -
167A LEU 3.4 2.7 - - - -
168A SER* 3.4 3.1 + - - -
169A ASP* 3.0 37.8 + - - -
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Residues in contact with GLU 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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165A GLY* 1.3 69.6 - - - -
167A LEU* 1.3 65.1 + - - +
169A ASP* 3.4 9.3 + - - +
170A ARG* 3.0 23.6 + - - +
173A ARG* 5.0 1.6 + - - -
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Residues in contact with LEU 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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162A LEU* 3.9 33.0 - - + -
165A GLY 3.4 0.2 - - - -
166A GLU* 1.3 77.1 - - - +
168A SER* 1.3 59.6 + - - +
170A ARG* 3.0 15.6 + - + +
171A VAL* 2.9 37.3 + - + +
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Residues in contact with SER 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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96A ARG* 2.9 21.5 + - - -
159A ALA* 2.6 29.6 + - - +
162A LEU* 4.1 14.0 - - - +
163A GLY 3.0 26.2 - - - -
165A GLY 3.4 4.0 + - - -
166A GLU 3.3 0.4 - - - -
167A LEU* 1.3 78.7 - - - +
169A ASP* 1.3 63.1 + - - +
171A VAL* 3.1 6.5 + - - +
172A LEU* 3.1 23.6 + - - +
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Residues in contact with ASP 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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93A ARG* 3.4 33.4 + - - +
96A ARG* 2.9 25.6 + - - +
165A GLY 3.0 24.5 + - - +
166A GLU* 3.6 9.6 - - - +
168A SER* 1.3 75.1 - - - +
170A ARG* 1.3 61.7 + - - +
172A LEU* 3.3 9.2 + - - +
173A ARG* 3.1 39.9 + - - +
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Residues in contact with ARG 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 GLU 3.0 13.9 + - - +
167A LEU* 3.0 18.3 + - + +
169A ASP* 1.3 74.9 - - - +
171A VAL* 1.3 54.5 + - - +
173A ARG* 3.3 28.8 + - + +
174A ALA* 2.8 38.6 + - + +
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Residues in contact with VAL 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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155A GLY* 3.5 28.7 - - - +
158A LEU* 3.9 22.7 - - + -
159A ALA* 3.9 10.8 - - + +
162A LEU* 3.7 23.8 - - + -
167A LEU* 2.9 25.6 + - + +
168A SER 3.1 7.8 + - - +
170A ARG* 1.3 74.1 - - - +
172A LEU* 1.3 63.8 + - - +
174A ALA* 3.9 5.1 - - - +
175A ALA* 3.0 24.5 + - + +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.9 36.6 - - + +
92A SER* 3.9 3.4 - - - +
93A ARG* 3.8 40.4 - - + +
96A ARG* 4.0 18.6 - - + +
155A GLY 4.2 1.8 - - - +
156A LEU* 3.9 17.9 - - + -
159A ALA* 3.6 19.1 - - + -
168A SER 3.1 13.8 + - - +
169A ASP* 3.6 8.1 - - - +
171A VAL* 1.3 78.0 - - - +
173A ARG* 1.3 62.5 + - - +
175A ALA* 3.8 4.9 - - - +
176A LYS* 3.0 31.1 + - - +
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Residues in contact with ARG 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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93A ARG* 5.9 2.4 - - - +
166A GLU 5.0 1.0 + - - -
169A ASP* 3.1 36.8 + - - +
170A ARG* 3.6 39.8 - - + +
172A LEU* 1.3 77.6 - - - +
174A ALA* 1.3 58.0 + - - +
176A LYS* 3.3 14.8 + - - +
177A GLN* 2.9 56.7 + - + +
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Residues in contact with ALA 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 ARG* 2.8 26.6 + - + +
171A VAL* 3.9 5.2 - - - +
173A ARG* 1.3 73.4 - - - +
175A ALA* 1.3 62.9 + - - +
177A GLN* 3.3 12.1 + - - +
178A ALA* 3.1 23.2 + - - +
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Residues in contact with ALA 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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91A LEU* 3.9 9.4 - - + -
151A LEU* 3.7 41.0 - - + +
155A GLY* 4.2 11.7 - - - -
171A VAL* 3.0 18.6 + - + +
172A LEU 3.8 2.9 - - - +
174A ALA* 1.3 74.6 - - - +
176A LYS* 1.3 66.5 + - - +
178A ALA* 3.2 12.5 + - - +
179A VAL* 3.5 13.9 + - - +
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Residues in contact with LYS 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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87A ALA* 3.7 11.9 - - + +
88A ALA* 3.8 25.7 + - + +
91A LEU* 3.2 47.9 + - + +
92A SER* 5.1 2.4 - - - +
172A LEU* 3.0 24.5 + - - +
173A ARG* 3.6 12.7 - - - +
175A ALA* 1.3 76.6 - - - +
177A GLN* 1.3 63.7 + - + +
179A VAL* 3.1 24.1 + - - +
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Residues in contact with GLN 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 ARG* 2.9 44.2 + - + +
174A ALA* 3.8 10.2 - - - +
175A ALA 3.3 0.4 - - - -
176A LYS* 1.3 77.7 - - + +
178A ALA* 1.3 59.7 + - - +
179A VAL 3.3 5.0 + - - +
180A ASN* 5.5 0.5 - - - +
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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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148A ASP* 4.5 0.3 - - - +
151A LEU* 3.7 25.7 - - + +
174A ALA 3.1 15.9 + - - +
175A ALA 3.7 5.2 - - - +
176A LYS 3.2 1.2 - - - -
177A GLN* 1.3 76.1 - - - +
179A VAL* 1.3 63.7 + - - +
180A ASN* 3.4 15.7 + - - +
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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