Contacts of the strand formed by residues 207 - 216 (chain B) in PDB entry 1HWG
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 GLU 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLU* 3.3 7.8 - - - +
181B VAL* 3.1 42.1 + - + +
205B ASP 3.9 0.6 + - - +
206B LYS* 1.3 75.5 - - - +
208B TYR* 1.3 67.6 - - - +
230B TYR* 3.8 24.1 - - - +
231B VAL 3.4 7.2 - - - +
232B THR* 3.3 34.8 + - + +
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Residues in contact with TYR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TYR* 4.7 8.5 - + + -
179B LYS* 3.3 23.6 - - - +
180B GLU* 3.3 32.8 + - + -
181B VAL* 4.4 2.9 - - - -
183B GLU* 5.1 0.7 - - - -
187B LYS* 5.9 3.4 - - - -
201B SER 4.9 0.3 + - - -
202B LEU* 3.6 39.1 - - + -
203B LYS* 2.9 53.0 + - - +
206B LYS* 3.7 13.4 - - + +
207B GLU* 1.3 75.7 - - - +
209B GLU* 1.3 62.5 + - - +
210B VAL* 5.1 3.8 - - + -
229B LEU 4.3 0.2 - - - -
230B TYR* 3.2 9.5 - - - -
231B VAL* 2.7 50.2 + - + +
233B LEU* 3.8 8.7 - - + -
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TYR* 3.1 3.5 - - - +
179B LYS* 2.7 71.4 + - + +
181B VAL* 3.6 14.6 - - + +
186B TRP* 3.4 21.3 - - + -
208B TYR* 1.3 75.1 - - - +
210B VAL* 1.3 60.9 + - - +
228B VAL* 3.3 21.2 - - + +
229B LEU 3.1 5.4 - - - -
230B TYR* 3.2 31.9 + - + -
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 5.2 1.9 - - + +
153B ILE* 5.1 4.0 - - + -
155B VAL* 4.5 19.7 - - + -
176B LEU* 3.7 31.4 - - + -
177B GLN 3.2 12.6 - - - +
178B TYR* 3.7 11.9 - - + -
199B VAL* 5.8 1.6 - - + -
202B LEU* 6.1 1.1 - - + -
208B TYR* 5.1 3.4 - - + -
209B GLU* 1.3 80.7 - - - +
211B ARG* 1.3 66.8 + - - +
212B VAL* 4.6 1.8 - - + -
227B GLU 4.1 0.9 - - - +
228B VAL* 3.4 4.2 - - - -
229B LEU* 2.8 49.5 + - + +
231B VAL* 4.3 20.4 - - + -
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Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 5.5 0.2 - - - -
177B GLN* 2.8 61.3 + - - +
186B TRP* 3.2 55.7 - - + +
210B VAL* 1.3 74.3 - - - +
212B VAL* 1.3 66.9 + - - +
225B PHE* 3.4 49.2 - - + +
226B SER* 4.0 7.9 - - - +
227B GLU 4.8 1.3 - - - -
228B VAL* 4.3 16.1 - - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PRO* 3.4 21.4 - - + +
137B LEU* 3.6 25.6 - - + -
157B TRP* 4.1 16.2 - - + -
174B TYR* 3.9 22.2 - - + -
175B GLU 3.3 14.6 - - - +
176B LEU* 3.9 24.9 - - + -
210B VAL* 4.6 2.5 - - + -
211B ARG* 1.3 80.5 - - - +
213B ARG* 1.3 62.8 + - - +
225B PHE* 4.1 2.9 - - - -
226B SER* 2.8 39.1 + - - +
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Residues in contact with ARG 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PRO* 4.0 7.4 - - - -
174B TYR* 3.3 5.1 - - - -
175B GLU* 2.9 72.9 + - + -
177B GLN* 4.2 4.0 - - - +
212B VAL* 1.3 75.6 - - - +
214B SER* 1.3 62.3 + - - +
222B TYR* 3.7 35.9 + - + +
223B GLY 3.9 17.1 + - - +
224B GLU 3.7 16.6 - - - +
225B PHE* 3.5 40.1 - - + -
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PRO* 3.9 13.8 - - - +
132B ASP 3.5 22.1 + - - -
134B PRO* 3.7 11.2 - - - +
160B PRO* 3.9 7.3 - - - +
172B LEU* 4.0 7.6 - - - +
173B GLU 3.6 5.4 - - - -
174B TYR* 3.1 27.9 - - - -
213B ARG* 1.3 73.7 - - - +
215B LYS* 1.3 62.5 + - - +
222B TYR* 3.0 25.1 - - - -
223B GLY 3.1 7.4 + - - +
224B GLU 4.8 1.0 + - - -
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 5.6 3.2 - - - -
131B PRO* 3.7 11.4 - - - -
172B LEU* 3.2 3.8 - - - -
173B GLU* 3.0 53.2 + - + +
214B SER* 1.3 77.7 - - - +
216B GLN* 1.3 70.7 + - - +
218B ASN* 4.6 5.8 - - - +
219B SER 3.1 31.1 + - - +
220B GLY 5.4 0.2 - - - -
221B ASN* 2.8 19.7 - - - +
222B TYR* 3.3 40.1 - - + +
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Residues in contact with GLN 216 (chain B).
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* 5.5 1.8 + - - -
175A THR* 5.7 0.4 + - - -
43B ARG* 4.5 26.7 - - - +
129B VAL* 4.0 4.9 - - + -
131B PRO* 3.7 2.6 - - - +
170B MET* 3.3 34.6 - - + +
171B VAL* 3.0 41.1 + - - +
172B LEU* 4.1 2.9 - - - -
215B LYS* 1.3 84.3 - - - +
217B ARG* 1.3 79.6 + - - +
218B ASN 3.1 3.3 + - - -
219B SER* 3.1 18.8 + - - +
221B ASN* 3.1 28.8 - - - +
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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