Contacts of the strand formed by residues 214 - 228 (chain A) in PDB entry 1NQG
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 TRP 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A ASN* 3.4 1.6 - - - -
210A PHE* 2.8 45.5 + + + -
211A THR* 3.1 34.6 + - + +
213A ALA* 1.3 77.3 - - + +
215A SER* 1.3 63.0 + - - +
254A LEU* 4.8 20.2 - - + -
255A ARG 3.8 13.2 - - - -
256A TYR* 3.4 46.0 - + + -
263A SER* 6.0 1.8 - - - -
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Residues in contact with SER 215 (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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208A HIS 3.3 5.2 + - - -
209A ASN* 2.9 26.5 + - - -
210A PHE* 3.5 6.0 - - - -
213A ALA 4.8 2.7 + - - -
214A TRP* 1.3 74.1 + - - +
216A GLY* 1.3 61.3 + - - +
254A LEU* 3.2 10.2 - - - +
255A ARG* 2.6 53.8 + - - -
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Residues in contact with GLY 216 (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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207A GLU* 3.4 2.8 - - - +
208A HIS* 2.5 49.6 + - - -
210A PHE* 4.0 11.0 - - - -
215A SER* 1.3 79.2 - - - +
217A PHE* 1.3 65.8 + - - +
253A GLY 3.5 8.5 - - - -
254A LEU* 4.0 3.4 - - - -
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Residues in contact with PHE 217 (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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206A LEU 3.1 9.4 - - - +
207A GLU* 4.5 9.6 - - + -
216A GLY* 1.3 77.1 - - - +
218A VAL* 1.3 74.6 + - - +
219A ARG* 3.5 43.7 - - + +
251A ASP* 3.9 3.4 - - + -
252A ALA* 3.0 21.2 - - - +
253A GLY* 3.0 62.5 + - - +
254A LEU* 4.3 0.4 - - - -
255A ARG* 4.2 27.4 - - + -
266A ILE* 4.2 20.2 - - + -
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Residues in contact with VAL 218 (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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204A GLY 4.1 0.3 - - - +
205A ALA* 3.4 1.7 - - - -
206A LEU* 2.8 47.2 + - + +
217A PHE* 1.3 84.3 - - - +
219A ARG* 1.3 70.1 + - - +
250A TRP* 4.8 12.8 - - + -
251A ASP 3.5 9.9 - - - +
252A ALA* 4.1 11.9 - - + -
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Residues in contact with ARG 219 (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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81A ASP* 2.2 54.0 + - - +
131A THR* 3.4 1.1 + - - -
132A THR* 4.2 13.5 + - - -
203A TYR* 3.1 24.0 - - + +
204A GLY 3.4 8.3 - - - +
205A ALA* 3.6 20.0 - - + -
206A LEU 5.1 0.2 - - - +
217A PHE* 3.5 36.3 - - + -
218A VAL* 1.3 75.9 - - - +
220A GLY* 1.3 60.1 + - - +
221A TYR* 4.7 11.7 + - + -
250A TRP* 3.2 15.1 - - - -
251A ASP* 2.9 60.8 + - + +
255A ARG* 5.4 4.0 - - - +
266A ILE* 6.0 1.2 - - - +
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Residues in contact with GLY 220 (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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203A TYR* 3.6 1.2 - - - -
204A GLY* 2.9 31.0 + - - +
219A ARG* 1.3 78.2 - - - +
221A TYR* 1.3 62.1 + - - +
249A SER 3.6 10.3 - - - -
250A TRP* 3.7 22.8 - - - -
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Residues in contact with TYR 221 (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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80A ILE* 3.3 28.8 + - + +
81A ASP* 4.5 11.1 + - - +
99A PHE* 4.6 12.7 - + - -
103A LEU* 3.9 24.2 - - + -
131A THR* 4.7 2.9 - - + -
202A LEU 3.2 14.6 - - - +
203A TYR* 3.3 35.4 - + + -
219A ARG* 4.7 10.5 + - + -
220A GLY* 1.3 82.2 - - - +
222A GLY* 1.3 61.4 + - - +
223A TYR* 4.9 7.4 - + - -
248A GLN* 3.3 4.3 - - - +
249A SER* 2.8 60.9 + - - +
250A TRP* 5.3 0.8 - - - -
251A ASP* 4.8 8.7 + - - -
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Residues in contact with GLY 222 (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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201A THR* 3.5 2.1 - - - +
202A LEU* 3.0 31.3 + - - +
221A TYR* 1.3 78.9 - - - +
223A TYR* 1.3 70.4 + - - +
247A SER 3.0 15.9 - - - -
248A GLN* 3.9 5.2 - - - -
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Residues in contact with TYR 223 (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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86A ASN* 4.3 3.1 + - - -
87A LEU* 3.0 31.2 - - + +
98A GLN* 3.3 23.3 - - + -
99A PHE* 3.9 15.5 - + - -
100A PRO* 3.6 22.9 - - + -
103A LEU* 4.9 5.2 - - + -
200A LYS 3.1 13.0 - - - +
201A THR* 3.7 13.7 - - - +
221A TYR* 4.9 10.3 - + - -
222A GLY* 1.3 83.5 - - - +
224A ASP* 1.3 60.8 - - - +
225A ASN* 3.2 28.7 - - - +
245A LEU* 4.0 4.7 - - + +
246A TYR* 3.7 2.3 - - - +
247A SER* 3.0 52.2 + - - +
249A SER* 5.7 1.1 - - - -
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Residues in contact with ASP 224 (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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198A LEU* 3.9 3.5 - - - +
199A SER* 4.0 0.2 - - - -
200A LYS* 2.9 39.3 + - + +
223A TYR* 1.3 71.7 - - - +
225A ASN* 1.3 61.8 + - - +
226A ARG* 2.8 25.6 + - - -
244A LYS* 2.8 25.3 + - - -
245A LEU 3.5 4.5 - - - -
246A TYR* 3.0 26.7 - - + -
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Residues in contact with ASN 225 (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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98A GLN* 2.7 57.8 + - - +
197A PHE* 3.9 4.2 - - + -
198A LEU 3.3 6.7 - - - +
199A SER* 2.8 30.4 + - - -
223A TYR* 3.2 20.1 - - - -
224A ASP* 1.3 82.6 + - - +
226A ARG* 1.3 69.7 + - - +
245A LEU* 2.7 42.6 + - + +
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Residues in contact with ARG 226 (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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196A GLY 4.6 0.2 - - - -
197A PHE* 3.6 2.6 + - - -
198A LEU* 3.0 46.1 + - + +
200A LYS* 5.5 4.9 - - - +
224A ASP* 2.8 33.5 + - - +
225A ASN* 1.3 75.2 - - - +
227A THR* 1.3 61.0 + - - +
228A ASN* 3.9 9.5 + - - +
242A THR* 6.2 2.5 - - - -
243A ARG 3.4 10.5 - - - +
244A LYS* 1.9 68.1 - - + +
246A TYR* 3.5 2.0 + - - -
277A TYR* 4.9 7.2 + - - +
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Residues in contact with THR 227 (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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61A GLY* 3.4 19.6 + - - -
62A GLN* 4.1 4.5 + - - -
98A GLN* 3.0 21.3 + - - +
196A GLY 3.4 6.5 - - - -
197A PHE* 2.6 50.7 - - + +
226A ARG* 1.3 75.5 - - - +
228A ASN* 1.3 64.3 + - - +
229A TYR* 3.5 6.1 + - - +
243A ARG* 3.2 27.8 + - + +
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Residues in contact with ASN 228 (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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62A GLN* 3.2 19.4 + - - -
193A ASP* 5.5 4.5 - - - +
194A ASN 5.8 0.2 + - - -
195A ASP* 3.3 13.4 - - - +
196A GLY* 3.3 22.6 + - - +
226A ARG* 4.9 6.9 + - - +
227A THR* 1.3 72.1 - - - +
229A TYR* 1.3 63.2 + - - +
241A ASP 3.6 5.8 - - - +
242A THR* 1.2 72.9 - - + +
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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