Contacts of the strand formed by residues 207 - 218 (chain B) in PDB entry 1HQR
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 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.7 2.0 - - - +
15A ASN* 3.0 30.2 + - + +
16A PRO* 5.2 2.2 - - + -
70A LEU* 2.8 29.8 - - + +
74A THR* 3.7 36.6 - - + +
79A TYR* 4.5 13.0 - + + -
80A THR 4.0 1.8 - - - -
81A PRO* 3.4 40.8 - - + -
205B PRO* 3.8 31.4 - - + -
206B ARG* 1.3 71.6 - - - +
208B LEU* 1.3 59.9 + - - +
232B TYR* 3.7 17.9 - - - +
233B ASN* 4.5 3.6 - - - +
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Residues in contact with LEU 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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12A PHE* 4.0 21.5 - - + -
13A TYR 3.6 9.2 - - - +
14A LEU* 3.3 28.0 - - + +
70A LEU* 3.2 4.2 - - - +
82A ILE* 3.6 16.4 - - + -
113A THR 4.2 0.2 - - - +
115A PRO* 4.0 20.2 - - + -
145A PHE* 4.2 3.6 - - + -
206B ARG 4.1 0.6 - - - -
207B PHE* 1.3 71.4 - - - +
209B GLN* 1.3 65.4 + - - +
210B GLN* 3.4 33.0 - - + +
232B TYR* 3.2 16.5 - - - -
233B ASN* 3.0 46.7 + - - +
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Residues in contact with GLN 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU 3.9 0.3 - - - +
12A PHE* 3.2 3.8 - - - -
13A TYR* 3.1 32.1 + - - +
66A ASP* 3.9 21.6 - - - +
69A ASN* 4.3 11.0 - - + -
70A LEU* 3.4 23.8 - - + +
73A MET* 4.2 16.8 - - - +
208B LEU* 1.3 77.4 - - - +
210B GLN* 1.3 94.8 + - - +
211B ASP* 3.3 17.2 + - - +
230B ASP* 3.4 19.8 + - - +
231B ILE 3.4 16.2 + - - +
232B TYR* 4.2 4.0 - - - +
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Residues in contact with GLN 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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11A GLU 3.4 3.8 - - - +
12A PHE* 3.7 20.2 - - + -
139A PRO* 5.3 1.2 - - - +
143A HIS* 3.2 29.0 + - - +
144A LEU 4.9 0.5 - - - +
145A PHE* 3.6 19.5 - - + -
208B LEU* 3.4 26.8 - - + +
209B GLN* 1.3 92.7 + - - +
211B ASP* 1.3 59.0 + - - +
212B LYS* 3.6 23.2 + - - -
229B ARG 3.6 0.2 - - - +
231B ILE* 2.8 51.1 + - + +
233B ASN 3.7 9.5 + - - -
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Residues in contact with ASP 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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9A GLN 3.3 1.6 - - - +
10A ALA* 3.6 0.7 - - - -
11A GLU* 2.7 54.1 + - + +
66A ASP* 2.7 25.1 - - - +
69A ASN* 4.3 5.0 + - - -
209B GLN* 3.3 13.0 + - - +
210B GLN* 1.3 74.1 - - - +
212B LYS* 1.3 64.0 + - - +
213B TYR* 4.1 16.4 - - + -
228B HIS* 3.0 18.3 + - - -
229B ARG 3.6 0.9 - - - -
230B ASP* 2.6 29.7 - - - +
414C THR* 5.2 1.2 - - - +
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Residues in contact with LYS 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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8A ILE* 4.3 12.8 - - + -
9A GLN 3.4 3.6 - - - -
10A ALA* 4.5 10.8 - - + -
11A GLU 5.3 0.2 - - - +
139A PRO* 3.8 25.4 - - + +
140A ARG 3.3 20.4 + - - +
141A GLU* 5.0 1.6 - - - +
143A HIS* 3.1 35.7 + - + +
210B GLN* 3.6 19.7 + - + +
211B ASP* 1.3 79.8 - - - +
213B TYR* 1.3 62.3 + - - +
214B GLU* 3.8 16.4 - - - +
227B LEU 3.4 6.1 - - - +
228B HIS* 3.4 1.1 - - - -
229B ARG* 3.0 39.8 + - + +
231B ILE* 3.9 14.4 - - + -
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Residues in contact with TYR 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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7A ILE 4.1 0.3 - - - +
8A ILE* 3.4 1.1 - - - -
9A GLN* 2.6 60.6 + - + +
11A GLU* 4.1 9.4 - - - -
211B ASP* 4.1 16.5 + - + -
212B LYS* 1.3 73.9 - - - +
214B GLU* 1.3 57.1 + - - +
226B PHE* 3.7 20.0 - + + -
227B LEU 3.7 3.4 - - - -
228B HIS* 3.4 40.7 + + - -
271B ARG* 3.7 11.1 + - - -
278B TYR* 3.5 21.7 + - + +
412C ILE* 3.3 30.7 - - + -
414C THR* 3.0 37.2 - - + +
415C PRO* 5.1 1.2 - - - +
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Residues in contact with GLU 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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6A VAL* 4.6 0.4 - - + -
7A ILE 3.4 2.9 - - - -
8A ILE* 3.6 30.8 - - + +
212B LYS* 4.3 13.5 - - - +
213B TYR* 1.3 74.7 - - - +
215B CYS* 1.3 62.2 + - - +
216B HIS* 3.4 22.0 + - - +
225B ARG 3.7 0.9 - - - +
226B PHE* 3.4 8.6 - - - -
227B LEU* 2.9 74.6 + - + +
229B ARG* 3.7 26.4 + - - -
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Residues in contact with CYS 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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5A HIS 3.9 0.3 - - - +
6A VAL* 3.2 9.0 - - - +
7A ILE* 2.7 41.0 + - + +
214B GLU* 1.3 72.8 - - - +
216B HIS* 1.3 61.9 + - - +
217B PHE* 3.5 18.5 - - + -
225B ARG 3.6 4.7 - - - -
278B TYR* 3.3 28.9 - - - -
279B CYS* 2.0 50.5 - - - -
282B ASN* 5.5 1.8 - - - -
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Residues in contact with HIS 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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3A GLU* 4.8 9.8 - - + +
5A HIS 3.8 2.9 - - - -
6A VAL* 3.3 29.7 - - + +
214B GLU* 3.4 34.5 + - + +
215B CYS* 1.3 78.8 - - - +
217B PHE* 1.3 62.9 + - - +
218B PHE* 4.1 17.1 + + + -
223B ARG 4.2 0.3 - - - +
224B VAL* 2.9 22.8 - - - +
225B ARG* 2.9 47.9 + - + +
227B LEU* 4.9 4.8 - - + +
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Residues in contact with PHE 217 (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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3A GLU 4.0 0.2 - - - -
4A GLU* 3.3 21.0 + - + +
5A HIS* 2.9 29.4 + - + +
7A ILE* 4.2 13.5 - - + -
215B CYS* 3.5 25.6 - - + -
216B HIS* 1.3 74.1 - - - +
218B PHE* 1.3 70.7 + - - +
220B GLY 3.3 13.5 - - - +
221B THR* 3.6 16.4 - - + -
223B ARG 4.6 0.2 - - - -
224B VAL* 3.8 17.7 - - + +
279B CYS* 3.1 39.9 - - + -
280B ARG* 3.8 5.4 - - - -
283B TYR* 3.2 45.8 - + + -
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Residues in contact with PHE 218 (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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3A GLU* 3.6 36.3 - - + -
4A GLU 5.0 1.6 - - - +
216B HIS* 4.2 19.7 - + + -
217B PHE* 1.3 85.2 - - - +
219B ASN* 1.3 76.3 + - + +
220B GLY 3.5 1.7 + - - +
222B GLU* 3.3 17.0 + - - +
223B ARG* 3.2 30.8 + - + +
224B VAL 5.0 1.6 - - - -
225B ARG* 4.7 22.4 - - + -
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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