Contacts of the strand formed by residues 189 - 194 (chain A) in PDB entry 1NM8
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 GLN 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 3.2 5.2 - - - -
186A HIS 3.0 26.4 + - - +
187A ASN* 3.1 17.5 - - - +
188A TYR* 1.3 79.4 - - - +
190A PHE* 1.3 60.2 + - - +
191A PHE* 3.5 20.1 - - + -
219A SER* 3.7 12.8 - - - +
221A GLN* 3.0 45.5 + - - +
224A LYS* 3.7 23.6 - - + +
359A LYS* 2.8 38.9 - - - +
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR* 4.8 10.1 - - + -
184A VAL 3.4 5.8 - - - -
185A VAL* 3.7 24.9 - - + -
188A TYR 3.9 15.5 - - - -
189A GLN* 1.3 71.5 - - - +
191A PHE* 1.3 68.9 + - - +
227A VAL* 5.5 0.4 - - + -
228A GLY* 4.3 12.6 - - - -
258A ILE* 3.8 24.7 - - + -
264A THR* 4.9 6.1 - - + -
298A GLY 4.9 1.1 - - - -
300A ARG 3.2 30.7 - - - -
301A TRP* 3.9 30.1 - + + -
359A LYS* 3.7 3.7 - - - +
360A LEU* 2.8 50.9 + - + +
362A PHE* 4.2 15.7 - + - -
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Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR* 3.2 8.3 - - - +
184A VAL* 2.8 34.2 + - - +
186A HIS 5.3 0.2 - - - -
189A GLN* 3.5 20.6 - - + -
190A PHE* 1.3 76.5 - - - +
192A GLU* 1.3 61.5 + - - +
193A LEU* 3.7 0.7 + - - -
215A ILE* 3.6 42.2 - - + -
218A SER* 3.6 42.0 - - - -
219A SER* 3.6 24.5 - - - -
356A MET* 6.5 0.2 - - - -
357A PRO* 4.2 10.8 - - + -
358A LYS 3.2 7.0 - - - +
359A LYS* 3.6 38.6 - - + -
360A LEU* 4.3 4.5 - - - +
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Residues in contact with GLU 192 (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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181A HIS* 3.6 30.8 + - + -
182A ILE 3.7 3.4 - - - -
183A THR* 4.5 3.4 - - - -
191A PHE* 1.3 70.1 - - - +
193A LEU* 1.3 58.9 + - - +
194A ASP* 4.1 10.5 + - - +
257A SER* 2.6 33.0 + - - +
357A PRO* 3.7 5.9 - - - +
358A LYS* 2.7 55.7 + - + +
360A LEU* 4.1 10.3 - - + +
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Residues in contact with LEU 193 (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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181A HIS* 3.2 3.9 - - - -
182A ILE* 2.8 63.3 + - + +
184A VAL* 4.4 5.8 - - + -
191A PHE 3.7 0.6 + - - +
192A GLU* 1.3 72.1 - - - +
194A ASP* 1.3 79.3 + - - +
195A VAL* 3.3 9.0 + - + +
203A LEU* 5.3 0.9 - - + -
208A ILE* 4.7 11.9 - - + -
211A GLN* 3.5 37.2 - - + +
212A LEU* 4.6 8.5 - - + -
215A ILE* 4.2 20.4 - - + -
357A PRO* 3.8 16.6 - - + -
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Residues in contact with ASP 194 (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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180A THR* 3.6 16.8 + - - +
181A HIS* 3.5 15.6 - - - +
192A GLU* 4.1 11.8 + - - +
193A LEU* 1.3 85.7 - - - +
195A VAL* 1.3 59.2 + - - +
196A TYR 3.5 13.7 - - - +
203A LEU* 3.8 13.8 - - + +
211A GLN* 5.4 0.5 - - - +
355A PRO* 5.7 9.6 - - + +
357A PRO* 6.1 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