Contacts of the strand formed by residues 174 - 179 (chain A) in PDB entry 3N2N
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 ILE 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 5.5 7.0 - - + +
142A ALA* 5.8 5.4 - - + -
143A SER 2.9 15.5 + - - +
144A VAL* 3.4 15.6 - - + +
145A ILE* 2.8 26.9 + - - +
172A GLY 4.7 4.5 - - - +
173A ALA* 1.3 76.3 - - - +
175A VAL* 1.3 62.0 + - - +
176A TYR* 3.7 26.5 - - + +
193A ASP* 3.6 17.0 - - - +
197A HIS* 3.8 14.1 - - + +
215A ILE* 6.2 2.2 - - + -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE* 3.8 34.5 - - + -
145A ILE* 3.7 18.6 - - + -
165A ALA 4.4 6.1 - - - +
168A SER* 4.6 3.1 - - - -
169A ARG* 3.6 27.6 - - + +
173A ALA* 4.7 1.6 - - + -
174A ILE* 1.3 76.7 - - - +
176A TYR* 1.3 71.3 + - - +
177A ALA* 5.8 0.4 - - - -
191A ILE* 3.7 17.9 - - + +
192A ALA* 3.4 5.9 - - - +
193A ASP* 2.8 38.7 + - - +
197A HIS* 3.4 11.5 - - - +
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Residues in contact with TYR 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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144A VAL* 3.6 29.6 - - + -
145A ILE 2.7 14.4 + - - +
146A ILE* 4.4 6.1 - - + -
147A ALA* 2.9 28.0 + - - +
174A ILE* 3.7 19.7 - - + +
175A VAL* 1.3 80.6 - - - +
177A ALA* 1.3 62.3 + - - +
192A ALA* 4.3 0.2 - - - -
196A ASP 4.8 1.1 - - - -
197A HIS* 3.3 43.7 + + - +
199A PHE* 3.6 19.5 - + + -
208A LEU* 3.8 23.1 - - + -
211A ILE* 3.6 41.9 - - + +
195B LYS* 5.3 2.1 + - - -
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Residues in contact with ALA 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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147A ALA* 3.4 11.9 - - + +
149A THR* 5.6 1.3 - - + -
176A TYR* 1.3 73.9 - - - +
178A VAL* 1.3 62.7 + - - +
179A GLY 4.1 0.7 - - - -
188A LEU* 4.1 33.4 - - + +
191A ILE* 5.3 4.7 - - + -
192A ALA* 3.9 18.7 - - + +
197A HIS 2.9 7.8 + - - +
198A VAL* 3.2 5.3 - - + +
199A PHE* 2.9 26.9 + - - +
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Residues in contact with VAL 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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65A PHE* 4.0 13.9 - - + -
146A ILE* 3.9 13.2 - - + -
147A ALA 2.8 10.4 + - - +
148A LEU* 3.4 27.5 - - + +
149A THR* 3.2 23.9 + - - +
177A ALA* 1.3 77.7 - - - +
179A GLY* 1.3 61.8 + - - +
180A VAL* 3.9 0.5 + - - +
188A LEU* 4.5 1.6 - - - -
199A PHE* 3.2 14.4 - - + +
200A PRO 4.0 2.9 - - - +
201A VAL* 3.6 27.6 - - + -
204A GLY* 4.5 0.7 - - - -
208A LEU* 3.6 31.2 - - + -
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Residues in contact with GLY 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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149A THR 3.3 8.1 - - - -
177A ALA 4.1 1.0 - - - -
178A VAL* 1.3 72.3 - - - +
180A VAL* 1.3 63.8 + - - -
183A PHE* 3.5 32.1 - - - -
188A LEU* 3.9 6.8 - - - +
199A PHE 2.8 13.7 + - - -
201A VAL* 2.9 28.6 + - - +
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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