Contacts of the strand formed by residues 174 - 181 (chain A) in PDB entry 2O5J
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LEU* 2.8 29.2 - - + +
45A LEU* 5.0 6.1 - - + +
48A ILE* 3.3 24.9 - - + -
172A SER* 3.0 27.8 + - - +
173A PRO* 1.3 80.7 - - + +
175A ARG* 1.3 63.8 + - - +
176A ARG 4.7 1.3 - - - +
177A VAL* 4.4 10.3 - - + -
199A ILE* 3.4 25.6 - - + -
200A TRP 3.1 19.1 - - - +
201A THR* 4.3 6.1 - - + -
202A ASP* 5.8 0.2 - - - -
210A ALA* 5.1 0.2 - - + -
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Residues in contact with ARG 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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45A LEU* 5.3 6.4 - - - +
173A PRO 4.2 1.0 + - - -
174A VAL* 1.3 75.1 - - - +
176A ARG* 1.3 106.5 + - + +
200A TRP* 3.2 12.8 + - + +
201A THR* 4.7 0.8 - - - +
202A ASP* 5.0 5.9 - - + +
693C GLU* 4.7 17.6 + - - +
697C ARG* 5.8 3.0 - - - +
865C THR* 5.9 2.4 - - - +
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Residues in contact with ARG 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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41A ARG* 5.2 0.4 - - - +
45A LEU* 5.4 4.3 - - - -
174A VAL* 3.7 0.8 - - - -
175A ARG* 1.3 128.1 - - + +
177A VAL* 1.3 65.3 + - - +
198A ARG 3.9 1.2 - - - +
199A ILE* 3.8 0.5 - - - -
200A TRP* 3.0 67.2 + - + +
863C ASP* 4.9 8.5 + - - +
864C GLY* 3.2 22.4 - - - +
865C THR* 3.1 40.2 - - - +
866C PRO* 5.4 4.0 - - + -
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Residues in contact with VAL 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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37A GLY 5.6 0.4 - - - +
41A ARG* 2.6 53.2 + - + +
44A LEU* 3.5 37.0 - - + -
45A LEU* 3.2 23.5 - - + +
174A VAL* 4.4 4.3 - - + -
176A ARG* 1.3 78.0 - - - +
178A ALA* 1.3 70.7 + - - +
179A PHE* 5.8 1.1 - - + -
197A LEU* 5.2 5.8 - - + -
198A ARG 3.5 7.0 - - - +
199A ILE* 4.2 13.0 - - + -
864C GLY* 3.1 15.7 - - - -
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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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41A ARG* 4.9 1.3 - - - +
177A VAL* 1.3 80.6 - - - +
179A PHE* 1.3 60.3 + - - +
180A GLN* 6.3 1.1 - - + -
197A LEU* 3.0 3.7 - - - -
198A ARG* 2.6 66.6 + - + +
200A TRP* 5.2 4.0 - - + -
860C HIS* 5.3 3.8 - - - -
862C PRO 4.1 9.6 - - - +
863C ASP* 4.5 1.6 - - - -
864C GLY* 3.6 19.5 - - - +
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Residues in contact with PHE 179 (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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33A GLY 4.3 0.4 - - - -
34A VAL* 4.0 17.0 - - + -
37A GLY* 3.6 15.9 - - - +
38A ASN* 3.4 28.5 - - + -
41A ARG* 4.6 17.0 - - + -
177A VAL* 5.8 1.1 - - + -
178A ALA* 1.3 76.3 - - - +
180A GLN* 1.3 69.9 + - - +
181A VAL* 3.4 24.7 - - + -
195A LEU* 3.4 28.3 - - + -
196A THR 3.4 4.5 - - - -
197A LEU* 3.8 10.8 - - + -
860C HIS* 5.4 5.4 + + - -
862C PRO 4.8 5.4 + - - +
937C ASP* 4.0 9.4 - - - +
939C ARG* 4.9 2.5 - - - -
975C TYR* 4.1 18.5 - + - -
980C GLY* 3.9 27.4 - - - -
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Residues in contact with GLN 180 (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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178A ALA* 5.8 1.3 - - + -
179A PHE* 1.3 78.7 - - - +
181A VAL* 1.3 61.4 + - - +
182A GLU* 3.0 27.5 + - - +
194A LYS 3.1 12.6 - - - +
195A LEU* 3.4 2.6 - - - +
196A THR* 3.1 27.4 + - - +
198A ARG* 5.7 8.1 - - + +
862C PRO* 5.0 11.4 - - - +
929C ARG* 3.8 17.2 + - - -
934C PHE* 4.3 15.1 - - + +
935C GLY 3.3 24.4 + - - +
936C VAL 4.0 4.2 - - - -
937C ASP* 2.7 22.1 + - - +
940C GLU* 3.4 13.4 + - - +
975C TYR* 5.5 0.2 - - - +
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Residues in contact with VAL 181 (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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33A GLY* 4.0 11.2 - - - -
34A VAL* 4.0 13.7 - - + +
179A PHE* 3.4 32.3 - - + -
180A GLN* 1.3 73.9 - - - +
182A GLU* 1.3 63.1 + - - +
193A ASP* 3.0 39.9 - - + +
194A LYS 3.2 8.1 - - - +
195A LEU* 4.6 0.7 - - + -
937C ASP* 3.5 8.1 + - - +
938C LYS* 2.9 42.6 + - + +
939C ARG* 4.4 11.4 - - - +
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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