Contacts of the helix formed by residues 171 - 179 (chain D) in PDB entry 3P3W
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 VAL 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169D LYS 4.6 6.5 - - - +
170D ASP* 1.3 78.5 + - - +
172D GLN* 1.3 69.1 + - + +
173D GLU 3.3 0.2 - - - -
174D PHE* 3.5 27.5 + - + +
175D ARG* 4.1 8.1 + - - +
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Residues in contact with GLN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ASP* 3.3 7.5 - - - +
171D VAL* 1.3 82.0 - - + +
173D GLU* 1.3 68.2 + - - +
175D ARG* 3.2 50.3 + - - +
176D ARG* 3.3 46.4 + - - +
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Residues in contact with GLU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C ASN* 6.3 1.8 - - - -
168D ILE* 3.7 31.9 - - + +
169D LYS 5.3 1.0 + - - -
170D ASP* 3.4 38.3 + - - +
171D VAL 3.3 0.6 - - - -
172D GLN* 1.3 73.8 - - - +
174D PHE* 1.3 65.0 + - - +
176D ARG* 3.3 35.9 + - - +
177D ILE* 3.3 24.1 - - + +
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Residues in contact with PHE 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LEU* 6.0 4.0 - - + -
165D VAL* 4.6 30.1 - - + -
168D ILE* 3.7 34.1 - - + +
169D LYS 5.7 2.0 - - - -
170D ASP 4.3 4.7 - - - -
171D VAL* 3.5 21.4 + - + +
172D GLN 3.2 0.6 - - - -
173D GLU* 1.3 77.9 - - - +
175D ARG* 1.3 63.0 + - + +
177D ILE* 3.2 18.0 + - + +
178D ILE* 3.3 19.7 + - + +
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Residues in contact with ARG 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D VAL 4.6 8.1 + - - +
172D GLN* 3.2 39.1 + - - +
174D PHE* 1.3 72.5 - - + +
176D ARG* 1.3 58.3 + - + +
177D ILE 3.0 9.4 + - - -
178D ILE* 3.5 15.6 - - + +
179D GLU* 3.3 39.6 + - - +
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Residues in contact with ARG 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C ASN* 5.7 3.2 + - - +
370C TYR* 5.8 1.8 + - - -
372C ASN* 5.5 4.0 - - - +
375C GLU* 3.7 29.2 + - - +
172D GLN* 3.3 41.2 + - + +
173D GLU* 3.3 38.0 + - - +
175D ARG* 1.3 75.2 - - + +
177D ILE* 1.3 65.5 + - + +
179D GLU* 4.4 11.0 - - - +
180D GLU* 3.5 20.9 - - - +
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Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 6.4 0.7 - - + -
136D LEU* 4.8 19.1 - - + -
163D ARG* 3.4 51.4 - - + +
165D VAL* 5.7 4.5 - - + -
168D ILE* 4.7 9.6 - - + -
173D GLU* 3.3 22.9 - - + +
174D PHE* 3.2 13.0 + - + +
175D ARG 3.0 0.6 - - - -
176D ARG* 1.3 87.0 - - + +
178D ILE* 1.3 71.2 + - + +
179D GLU 3.3 1.6 - - - -
180D GLU* 3.3 17.4 + - - +
181D MET* 3.4 21.0 - - + +
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Residues in contact with ILE 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LEU* 6.0 6.3 - - + -
174D PHE* 3.3 17.5 - - + +
175D ARG* 3.5 26.2 - - + +
177D ILE* 1.3 81.8 - - + +
179D GLU* 1.3 69.4 + - + +
180D GLU 3.3 1.3 + - - -
181D MET* 3.7 15.5 + - + +
182D ASP* 3.0 20.4 - - - +
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Residues in contact with GLU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ARG* 3.3 29.6 + - - +
176D ARG* 4.4 10.6 - - - +
178D ILE* 1.3 85.4 - - + +
180D GLU* 1.3 61.2 + - - +
181D MET 3.3 1.1 + - - -
182D ASP* 3.8 23.6 + - - +
183D ARG* 4.7 1.7 + - - +
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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