Contacts of the strand formed by residues 181 - 185 (chain D) in PDB entry 4M3P
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 181 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 3.5 9.0 - - + +
171D VAL* 4.3 23.1 - - + -
174D LEU* 3.8 29.6 - - + +
175D ILE* 3.7 36.6 - - + +
179D LYS 3.3 17.3 - - - +
180D PRO* 1.3 76.2 - - - +
182D ALA* 1.3 71.3 + - - +
209D GLY 4.7 2.0 - - - +
210D ALA* 3.4 4.8 - - - -
211D SER* 3.0 31.6 + - - +
212D ILE* 3.6 4.2 + - - -
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Residues in contact with ALA 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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155D PHE* 4.7 5.3 - - + -
156D LEU 2.9 11.1 + - - +
157D ILE* 3.3 14.4 - - + -
158D ALA 2.8 25.1 + - - -
181D VAL* 1.3 79.4 - - - +
183D ALA* 1.3 62.5 + - - +
212D ILE* 3.3 33.1 - - + +
245D MET* 3.9 19.5 - - + -
295D TYR* 5.4 0.2 - - + -
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Residues in contact with ALA 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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158D ALA* 3.2 9.6 - - + +
167D ALA* 6.0 1.6 - - + -
171D VAL* 3.7 28.5 - - + -
182D ALA* 1.3 77.5 - - - +
184D THR* 1.3 62.5 + - - +
205D LEU* 3.9 22.1 - - + +
210D ALA* 4.1 10.1 - - + -
212D ILE 2.9 8.9 + - - -
213D ILE* 3.2 7.8 - - - +
214D GLY 3.1 21.0 + - - +
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Residues in contact with THR 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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157D ILE* 5.2 1.5 - - + +
158D ALA 2.8 14.9 + - - +
159D GLU* 3.3 22.3 + - - +
160D TYR 3.5 3.6 + - - -
161D PHE* 3.9 5.0 + - - -
183D ALA* 1.3 78.7 - - - +
185D MET* 1.3 64.6 + - - +
214D GLY 3.2 14.6 - - - +
215D VAL 3.6 18.4 - - - +
216D ASN* 2.6 29.6 + - + +
245D MET* 3.6 37.6 - - + +
247D GLN* 5.7 0.6 + - + -
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Residues in contact with MET 185 (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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161D PHE* 3.0 33.9 - - + +
162D GLU 3.8 7.0 - - - +
163D HIS 3.6 7.2 - - - +
164D VAL* 3.4 51.6 - - + +
167D ALA* 4.5 3.8 - - + -
184D THR* 1.3 79.0 - - - +
186D CYS* 1.3 59.2 + - - +
187D ILE* 3.2 27.5 + - + -
192D ASP* 4.4 2.2 - - + -
201D CYS* 4.0 15.7 - - - -
205D LEU* 4.1 19.3 - - + -
214D GLY 3.1 8.7 + - - +
215D VAL* 3.2 10.9 - - - +
216D ASN* 3.1 18.9 + - - -
231D MET* 4.5 3.4 - - + -
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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