Contacts of the strand formed by residues 207 - 214 (chain B) in PDB entry 2XN9
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 HIS 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B TRP 3.7 1.5 + - - +
161B VAL* 3.4 7.6 - - - +
162B ASN* 2.8 44.0 + - - +
163B GLY* 4.9 6.8 + - - -
205B ARG 3.6 0.4 + - - +
206B ASN* 1.3 74.7 - - - +
208B PHE* 1.3 66.3 + - - +
209B ARG* 4.2 15.4 - - + +
238B GLU* 2.9 46.8 + - + +
239B ALA 3.9 5.6 - - - -
240B TRP* 3.4 50.6 - + + -
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Residues in contact with PHE 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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143B LEU* 3.7 26.9 - - + -
159B TRP* 4.9 4.9 - - + -
160B TRP 3.6 2.5 - - - -
161B VAL* 3.8 21.8 - - + -
194B LEU* 3.9 10.3 - - + -
196B VAL* 4.3 13.5 - - + -
200B PHE* 3.8 36.1 - + - -
201B TRP* 3.7 37.9 - + - -
206B ASN* 3.6 23.6 - - + -
207B HIS* 1.3 76.4 - - - +
209B ARG* 1.3 63.1 + - - +
238B GLU* 3.2 6.9 - - - +
239B ALA 2.8 46.6 + - - +
241B GLY* 3.8 5.8 - - - -
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Residues in contact with ARG 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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158B SER 3.8 0.2 - - - +
159B TRP* 3.3 12.6 - - - -
160B TRP* 2.8 54.0 + - + +
207B HIS* 4.2 8.3 - - + -
208B PHE* 1.3 76.5 - - - +
210B CYS* 1.3 69.7 + - - +
211B GLN* 2.8 31.6 + - + -
234B ILE* 4.1 8.7 - - - +
236B SER* 2.6 36.0 + - - -
237B ALA 3.6 3.1 - - - -
238B GLU* 3.0 37.4 + - + +
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Residues in contact with CYS 210 (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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125B VAL* 4.1 5.9 - - + +
127B VAL* 3.8 14.5 - - + +
145B CYS* 2.0 53.6 - - + -
157B LEU* 3.9 22.4 - - - -
158B SER 3.6 2.9 - - - -
159B TRP* 4.1 9.9 - - + -
209B ARG* 1.3 73.0 - - - +
211B GLN* 1.3 61.7 + - - +
212B VAL* 4.3 2.5 - - - -
235B VAL 4.1 0.2 - - - +
236B SER* 3.1 7.3 - - - -
237B ALA 2.9 28.8 + - - +
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Residues in contact with GLN 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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156B GLU 3.6 1.4 - - - +
157B LEU* 3.1 4.5 - - - +
158B SER* 2.8 47.1 + - - +
160B TRP* 3.6 36.2 + - + +
209B ARG* 2.8 31.5 + - - +
210B CYS* 1.3 75.5 - - - +
212B VAL* 1.3 63.2 + - - +
213B GLN* 4.1 3.1 - - - +
234B ILE* 3.8 36.5 - - + +
235B VAL 3.8 2.0 - - - -
236B SER* 3.9 4.9 - - - +
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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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123B PRO* 3.7 23.8 - - + -
125B VAL* 3.6 31.0 - - + -
147B ALA* 4.1 8.3 - - + -
155B VAL* 4.0 24.5 - - + -
156B GLU 3.5 4.0 - - - +
157B LEU* 3.7 28.0 - - + -
210B CYS* 4.3 1.6 - - - -
211B GLN* 1.3 77.5 - - - +
213B GLN* 1.3 64.9 + - - +
214B PHE* 3.4 2.4 + - - +
233B GLN 3.6 0.2 - - - +
234B ILE* 3.4 4.2 - - - -
235B VAL* 2.7 40.9 + - - +
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Residues in contact with GLN 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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154B HIS 4.1 0.2 - - - +
155B VAL* 3.2 7.4 - - - +
156B GLU* 2.8 47.3 + - + +
211B GLN* 4.1 3.6 - - - +
212B VAL* 1.3 72.2 - - - +
214B PHE* 1.3 82.2 + - - +
215B TYR* 3.4 33.8 - - + +
232B THR* 3.6 13.9 - - - +
233B GLN* 3.2 19.1 + - - +
234B ILE* 3.3 27.1 - - + +
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Residues in contact with PHE 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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120B VAL* 4.1 3.4 - - + -
121B PHE 3.3 24.5 - - - -
122B PRO* 3.8 18.2 - - + -
123B PRO* 3.5 30.5 - - + -
150B PHE* 4.4 0.4 - - + -
151B TYR 3.4 18.2 - - - -
152B PRO* 3.8 15.5 - - + -
154B HIS 3.8 8.1 - - - -
155B VAL* 4.0 8.1 - - + -
212B VAL 3.4 0.6 + - - +
213B GLN* 1.3 91.2 + - - +
215B TYR* 1.3 70.7 + - - +
216B GLY* 3.4 27.4 - - - -
230B PRO 3.7 6.7 - - - -
231B VAL 3.4 21.8 - - - -
232B THR* 3.3 2.6 - - - +
233B GLN* 2.8 27.9 + - + +
235B VAL* 5.5 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