Contacts of the strand formed by residues 172 - 177 (chain A) in PDB entry 2NUP
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 MET 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PHE* 3.4 3.5 - - - +
170A GLY 2.9 23.9 + - - -
171A ARG* 1.3 116.8 - - + +
173A VAL* 1.3 64.5 + - - +
174A GLN* 4.3 6.5 + - + +
188A VAL* 3.5 26.2 - - + -
189A PHE 3.5 4.3 - - - +
190A ARG* 4.1 23.1 - - + +
191A GLY 4.7 0.2 - - - -
250A ASP* 5.1 0.4 + - - -
252A TRP* 3.6 30.4 - - + +
577B PHE* 4.1 15.5 - - + -
578B ILE 4.7 5.2 - - - +
579B PRO 4.1 9.2 - - - +
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Residues in contact with VAL 173 (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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167A ILE* 3.9 22.0 - - + -
168A THR 3.9 3.4 - - - +
169A PHE* 4.0 7.2 - - + -
172A MET* 1.3 77.8 - - - +
174A GLN* 1.3 63.8 + - - +
175A VAL* 4.2 1.3 - - + -
187A TYR 3.3 3.6 - - - +
188A VAL* 3.4 2.3 - - - -
189A PHE* 2.7 39.4 + - - +
191A GLY* 4.0 20.6 - - - -
263A SER* 4.2 4.5 - - - -
266A VAL* 4.3 4.9 - - + -
267A ALA* 3.9 30.7 - - + +
270A ILE* 3.9 27.4 - - + -
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Residues in contact with GLN 174 (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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167A ILE* 3.2 8.7 - - - +
168A THR* 2.7 53.7 + - - +
169A PHE* 6.1 0.8 - - - +
172A MET* 5.2 5.2 + - + +
173A VAL* 1.3 77.8 - - - +
175A VAL* 1.3 63.4 + - - +
176A HIS* 3.5 14.9 - - - +
186A SER* 2.9 28.6 + - - +
187A TYR 3.4 2.9 - - - -
188A VAL* 4.3 20.8 - - + +
251A PRO* 5.6 9.5 - - - +
566B GLN* 5.8 1.3 + - - +
568B LEU* 4.4 10.9 - - - +
579B PRO 5.9 0.4 + - - -
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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
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166A LEU 4.9 0.7 - - - +
167A ILE* 4.0 13.0 - - + -
173A VAL* 4.9 1.6 - - + -
174A GLN* 1.3 72.6 - - - +
176A HIS* 1.3 62.3 + - - +
177A GLU 3.7 0.7 + - - -
186A SER* 3.3 1.5 - - - -
187A TYR* 2.8 37.6 + - + +
189A PHE* 4.1 18.8 - - + -
204A LEU* 4.3 10.8 - - + -
229A PHE* 3.5 34.9 - - + -
270A ILE* 3.6 30.5 - - + -
274A LEU* 4.2 19.7 - - + -
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Residues in contact with HIS 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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166A LEU* 3.0 42.2 + - + +
168A THR* 3.1 28.3 + - + +
174A GLN* 3.5 22.3 + - - +
175A VAL* 1.3 73.3 - - - +
177A GLU* 1.3 61.0 + - - +
178A LEU* 3.5 12.8 + - + +
185A LYS 3.8 7.2 + - - +
186A SER* 3.7 18.2 - - - -
229A PHE* 3.3 20.7 - - - +
243A LEU* 3.6 38.6 - - + +
247A LEU* 5.1 3.1 - - + -
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Residues in contact with GLU 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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175A VAL 3.7 2.2 + - - -
176A HIS* 1.3 70.7 - - - +
178A LEU* 1.3 66.7 + - - +
179A GLY 3.8 0.7 + - - -
180A CYS* 3.7 20.5 + - + +
184A SER* 5.4 0.7 - - - -
185A LYS* 3.0 60.6 + - + +
187A TYR* 3.8 8.0 + - + -
228A ARG* 3.1 63.8 + - + +
229A PHE* 3.8 12.1 - - + -
231A GLN* 5.9 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