Contacts of the strand formed by residues 180 - 184 (chain D) in PDB entry 3WF4
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 180 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D LEU* 4.4 18.6 - - + -
118D VAL* 3.4 25.4 - - + +
120D LEU* 4.0 20.0 - - + -
169D MET* 5.3 1.8 - - + +
172D LEU* 2.8 28.8 + - + +
173D LEU* 3.6 25.0 - - + +
174D TYR* 2.8 24.4 + - - +
175D GLN* 4.3 2.6 - - - +
178D GLY 3.5 0.8 - - - -
179D PRO* 1.3 71.3 - - + +
181D ILE* 1.3 61.2 + - - +
182D THR 3.5 19.5 - - - +
183D VAL* 4.0 6.7 - - + -
215D VAL* 5.7 0.9 - - - +
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Residues in contact with ILE 181 (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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32D PHE* 3.4 54.8 - - + +
48D PHE* 4.0 16.8 - - + -
50D TYR* 4.1 17.0 - - + -
79D ALA* 4.9 0.2 - - + -
117D LEU* 4.0 30.7 - - + -
118D VAL 2.9 20.6 + - - +
119D ILE* 4.2 9.2 - - + -
174D TYR* 4.1 13.2 - - + -
175D GLN* 5.4 2.8 + - - +
179D PRO 3.7 11.7 - - - +
180D VAL* 1.3 75.3 - - - +
182D THR* 1.3 72.0 + - + +
215D VAL* 4.9 3.3 - - - +
216D VAL* 3.8 10.8 + - - +
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Residues in contact with THR 182 (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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32D PHE* 3.8 18.4 - - + -
41D PHE* 4.2 14.1 - - + -
50D TYR* 4.6 4.4 + - + -
119D ILE* 3.4 19.6 - - - +
120D LEU 3.1 21.7 + - - -
180D VAL* 3.5 5.2 - - - +
181D ILE* 1.3 90.6 - - + +
183D VAL* 1.3 66.5 + - - +
216D VAL* 3.4 24.0 - - + +
218D PHE* 3.3 26.6 - - + -
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Residues in contact with VAL 183 (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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120D LEU* 3.3 12.1 - - + +
122D PRO* 3.6 26.0 - - + -
166D LEU* 6.0 0.2 - - + -
173D LEU* 4.7 2.0 - - + -
180D VAL* 4.0 15.3 - - + -
182D THR* 1.3 79.9 - - - +
184D GLN* 1.3 63.6 + - - +
185D VAL 3.7 0.3 + - - -
207D PHE* 3.7 25.4 - - + -
211D LEU* 4.2 13.9 - - + -
215D VAL* 3.8 20.4 - - + -
216D VAL 3.0 5.9 + - - -
217D LEU* 3.5 15.0 - - + +
218D PHE* 3.0 25.9 + - - -
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Residues in contact with GLN 184 (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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83D TYR* 4.7 1.4 - - - -
120D LEU 2.9 9.3 + - - -
121D ARG* 2.9 43.2 + - + +
122D PRO* 3.2 24.8 - - - +
123D GLY 4.3 1.7 + - - -
183D VAL* 1.3 72.7 - - - +
185D VAL* 1.3 64.4 + - - +
186D GLU 2.7 26.2 + - - +
187D ASN* 3.1 29.9 + - - +
207D PHE* 4.0 0.5 - - - -
218D PHE* 3.2 32.8 - - + +
220D THR* 2.6 32.2 + - - +
267D SER* 4.6 0.2 - - - -
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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