Contacts of the strand formed by residues 197 - 209 (chain A) in PDB entry 1NQF
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 PHE 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A SER* 3.6 37.7 - - - +
61A GLY* 4.0 10.5 - - - -
97A SER 4.4 8.7 - - - -
98A GLN* 3.3 32.3 - - - -
173A ALA 3.8 2.9 - - - +
174A HIS* 2.9 5.5 - - - -
175A THR* 2.9 38.0 + - + +
176A HIS* 4.4 2.2 - - - +
196A GLY* 1.3 73.7 - - - +
198A LEU* 1.3 60.6 + - - +
199A SER* 4.3 15.7 - - - -
225A ASN* 3.8 18.6 - - + -
226A ARG 3.1 10.1 - - - -
227A THR* 2.5 31.2 - - + +
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Residues in contact with LEU 198 (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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172A TYR* 3.0 42.6 - - + +
174A HIS* 3.3 13.7 - - + +
197A PHE* 1.3 76.0 - - - +
199A SER* 1.3 81.1 + - - +
200A LYS* 3.7 19.3 - - + +
224A ASP* 4.4 3.6 - - - +
225A ASN* 3.2 5.9 - - - +
226A ARG* 2.8 55.9 + - + +
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Residues in contact with SER 199 (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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100A PRO* 4.6 8.4 - - - +
171A ASP* 3.9 2.4 + - - +
172A TYR* 3.4 4.5 - - - -
173A ALA* 2.4 56.5 + - - +
197A PHE* 4.3 13.9 - - - -
198A LEU* 1.3 83.5 - - - +
200A LYS* 1.3 60.2 + - - +
201A THR* 3.6 13.9 + - - -
223A TYR* 4.6 1.4 - - - +
225A ASN* 3.0 24.3 + - - -
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Residues in contact with LYS 200 (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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171A ASP 3.5 4.7 - - - +
172A TYR* 3.7 26.2 - - + -
198A LEU* 3.8 24.2 - - + -
199A SER* 1.3 73.3 + - - +
201A THR* 1.3 63.3 + - - +
202A LEU* 6.4 0.4 - - + -
223A TYR* 3.1 5.2 - - - +
224A ASP* 2.8 50.7 + - + +
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Residues in contact with THR 201 (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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100A PRO* 3.6 22.3 - - + +
102A ALA* 5.3 0.2 - - - -
103A LEU* 3.6 40.6 - - + -
169A LEU* 3.8 2.6 - - + +
170A GLY* 3.1 2.4 - - - -
171A ASP* 2.8 52.4 + - - -
199A SER* 3.6 8.3 + - - -
200A LYS* 1.3 79.5 + - - +
202A LEU* 1.3 77.2 + - - +
222A GLY 3.6 10.3 - - - +
223A TYR* 3.6 3.4 - - + +
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Residues in contact with LEU 202 (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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169A LEU 3.6 2.7 - - - +
170A GLY* 3.8 13.5 - - - -
171A ASP 4.9 0.2 - - - +
200A LYS* 6.4 0.2 - - + -
201A THR* 1.3 92.8 - - - +
203A TYR* 1.3 62.9 + - - +
221A TYR* 3.3 5.4 - - - +
222A GLY 2.9 36.1 + - - +
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Residues in contact with TYR 203 (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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103A LEU* 3.7 20.0 - - + -
131A THR* 2.6 43.5 + - - -
132A THR* 4.3 3.5 + - - +
133A ARG* 6.6 0.2 - - - -
167A THR* 4.7 15.3 - - + -
168A LEU* 3.3 4.3 - - - +
169A LEU* 2.8 57.9 + - + +
202A LEU* 1.3 77.0 - - - +
204A GLY* 1.3 63.1 + - - +
205A ALA* 4.0 21.1 - - + +
219A ARG* 3.3 24.9 - - + +
220A GLY 3.7 4.3 - - - -
221A TYR* 3.5 29.2 - + + -
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Residues in contact with GLY 204 (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 THR 3.1 10.3 - - - -
168A LEU* 4.0 12.6 - - - -
203A TYR* 1.3 80.7 - - - +
205A ALA* 1.3 62.6 + - - +
219A ARG* 4.1 0.7 - - - +
220A GLY 3.2 31.5 + - - +
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Residues in contact with ALA 205 (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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165A ARG 4.3 0.2 - - - -
166A VAL* 3.2 2.6 - - - +
167A THR* 2.8 37.9 + - - +
168A LEU* 5.1 0.2 - - - +
203A TYR* 4.0 15.9 - - + +
204A GLY* 1.3 75.9 - - - +
206A LEU* 1.3 76.7 + - - +
207A GLU* 4.7 11.4 - - + +
217A PHE* 6.4 0.2 - - + -
218A VAL* 3.5 12.8 - - - +
219A ARG* 4.0 14.6 - - + -
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Residues in contact with LEU 206 (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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160A LEU* 5.1 2.0 - - + -
164A THR* 4.3 16.2 - - + -
165A ARG 3.2 3.4 - - - +
166A VAL* 3.3 29.4 - - + -
205A ALA* 1.3 89.4 - - - +
207A GLU* 1.3 62.4 + - - +
208A HIS* 4.0 1.8 - - + -
216A GLY 3.8 0.3 - - - +
217A PHE* 3.2 9.2 - - - +
218A VAL* 2.8 49.1 + - + +
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Residues in contact with GLU 207 (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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132A THR* 3.5 19.9 - - + +
133A ARG 4.3 1.0 + - - +
163A LYS 3.5 2.8 - - - +
164A THR* 3.0 3.9 - - - -
165A ARG* 2.6 103.6 + - + +
167A THR* 3.7 14.2 + - - -
205A ALA* 4.7 11.4 - - + +
206A LEU* 1.3 78.7 - - - +
208A HIS* 1.3 59.0 + - - +
209A ASN* 5.5 3.1 - - - +
216A GLY 3.7 4.0 - - - +
217A PHE* 4.6 10.1 - - + -
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Residues in contact with HIS 208 (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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163A LYS* 3.8 17.5 - - + +
164A THR* 2.7 34.1 - - + +
206A LEU* 4.0 1.7 - - + -
207A GLU* 1.3 75.1 - - - +
209A ASN* 1.3 76.8 + - - +
210A PHE* 3.4 42.7 + + + -
215A SER* 3.5 2.6 - - - -
216A GLY 2.8 40.9 + - - +
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Residues in contact with ASN 209 (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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163A LYS* 3.2 41.4 + - + +
207A GLU* 5.5 2.4 - - - +
208A HIS* 1.3 75.3 + - - +
210A PHE* 1.3 67.1 + - - +
211A THR 3.1 21.3 + - - +
212A ASP* 4.9 2.4 - - - +
213A ALA 4.9 3.0 - - - +
214A TRP 3.7 9.1 + - - +
215A SER* 3.8 16.3 + - - -
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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