Contacts of the strand formed by residues 160 - 173 (chain B) in PDB entry 1P7L
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 LEU 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B GLN* 3.5 37.9 - - + +
151B VAL* 3.6 17.0 - - + -
152B ARG* 3.4 26.7 - - + +
157B LEU* 3.0 34.2 + - + +
158B PRO 3.8 6.1 - - - +
159B TRP* 1.3 108.1 - - + +
161B ARG* 1.3 63.8 + - - +
162B PRO* 4.8 0.2 - - - +
187B THR* 3.7 26.5 - - + +
188B GLN 3.9 2.0 - - - +
202B VAL* 5.2 0.7 - - + -
206B ILE* 4.2 4.5 - - + -
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Residues in contact with ARG 161 (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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81B ASP* 3.3 46.0 + - - +
82B MET* 3.9 27.3 - - + +
148B GLN* 3.0 23.2 + - - -
152B ARG* 3.5 4.7 - - - -
159B TRP* 4.2 3.2 + - - +
160B LEU* 1.3 76.5 + - - +
162B PRO* 1.3 75.4 - - + +
163B ASP 3.4 3.9 + - - +
188B GLN* 3.0 43.0 + - + +
189B HIS 3.5 30.8 + - - -
190B SER* 3.8 22.2 - - - +
191B GLU 5.0 1.0 - - - +
231B VAL* 4.7 8.3 + - - +
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Residues in contact with PRO 162 (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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11B SER* 2.6 29.6 + - - -
13B GLY* 3.4 12.3 - - - -
75B ILE 4.3 3.4 - - - +
76B GLY* 3.9 30.3 - - - +
77B TYR* 3.6 31.9 - - + +
82B MET* 4.4 7.9 - - - -
148B GLN* 4.0 1.4 + - - -
152B ARG* 3.4 30.7 + - - +
161B ARG* 1.3 95.4 - - + +
163B ASP* 1.3 55.0 + - - +
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Residues in contact with ASP 163 (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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13B GLY 3.6 13.0 - - - -
14B HIS* 3.7 11.3 - - - +
15B PRO* 3.9 5.3 - - - +
77B TYR* 3.2 17.6 + - - +
161B ARG 3.4 2.9 - - - +
162B PRO* 1.3 77.8 - - - +
164B ALA* 1.3 68.0 + - - +
187B THR* 3.6 0.2 - - - -
188B GLN* 2.8 44.9 + - + +
230B PHE* 3.7 3.9 - - - -
233B GLY* 3.7 4.2 - - - -
234B GLY* 2.8 22.0 + - - +
484B ANP 2.6 39.2 + - - -
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Residues in contact with ALA 164 (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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10B VAL* 4.1 0.7 - - - +
11B SER* 2.8 38.5 + - - -
14B HIS* 4.5 0.9 - - - +
145B VAL* 4.5 3.6 - - + -
148B GLN* 3.6 31.4 - - + +
163B ASP* 1.3 83.9 + - - +
165B LYS* 1.3 69.6 + - - +
185B LEU* 5.5 2.0 - - + -
186B SER 3.1 13.2 - - - +
187B THR* 3.8 6.3 - - - +
230B PHE* 4.8 1.8 - - - -
484B ANP 4.6 1.6 - - - -
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Residues in contact with LYS 165 (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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118A ASP* 3.0 17.4 + - - -
119A GLN* 3.5 35.7 + - - +
8B GLU* 4.2 4.0 + - - -
9B SER 3.5 4.5 - - - +
10B VAL* 3.3 22.6 - - + +
14B HIS* 3.7 6.7 + - + -
145B VAL* 4.1 3.1 - - - -
164B ALA* 1.3 81.5 - - - +
166B SER* 1.3 61.2 + - - +
185B LEU* 3.6 3.9 - - - +
186B SER* 2.6 43.1 + - - +
245B LYS* 4.9 0.2 - - - +
484B ANP 2.9 71.3 + - - +
487B MG 4.1 4.8 - - - -
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Residues in contact with SER 166 (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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119A GLN* 3.3 7.8 + - - +
8B GLU* 3.2 3.5 - - - -
9B SER* 2.7 37.5 + - - -
141B ALA* 2.9 30.4 + - - +
144B LEU* 3.9 11.9 - - - -
145B VAL* 3.7 12.7 - - - +
165B LYS* 1.3 76.4 - - - +
167B GLN* 1.3 57.7 + - - +
184B VAL 3.3 4.7 - - - -
185B LEU* 3.7 17.9 - - - -
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Residues in contact with GLN 167 (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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119A GLN* 3.5 11.7 - - - +
120A GLY* 2.8 32.3 + - - -
121A LEU* 4.9 0.3 - - - +
300A TYR 2.7 28.0 + - - +
308A THR* 3.3 23.4 + - - +
6B THR* 3.6 18.8 - - + +
7B SER 3.4 13.2 - - - +
8B GLU* 4.1 7.2 - - + +
166B SER* 1.3 74.5 - - - +
168B VAL* 1.3 71.5 + - - +
169B THR* 5.0 2.0 - - + +
182B ALA 4.1 0.4 - - - +
183B VAL* 3.6 0.2 - - - -
184B VAL* 2.5 59.4 + - + +
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Residues in contact with VAL 168 (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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5B PHE 4.2 0.3 - - - +
6B THR* 3.3 0.9 - - - +
7B SER* 3.1 33.2 + - - +
137B PRO 5.2 3.4 - - - +
140B TYR* 5.1 1.6 - - + -
141B ALA* 4.5 13.0 - - + +
144B LEU* 3.4 31.6 - - + -
167B GLN* 1.3 79.7 - - - +
169B THR* 1.3 67.2 + - - +
170B PHE* 3.6 28.1 + - + -
180B ILE* 3.3 30.5 - - + -
182B ALA 3.7 5.4 - - - +
183B VAL* 4.4 8.3 - - + -
184B VAL 5.3 0.2 - - - +
211B LEU* 5.0 4.7 - - + -
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Residues in contact with THR 169 (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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299A SER* 4.6 1.3 - - - +
308A THR* 4.3 16.4 + - - +
309A SER* 4.4 4.9 - - - -
4B LEU* 4.6 4.7 - - - +
5B PHE 3.5 6.3 - - - -
6B THR* 3.3 35.4 - - + +
167B GLN* 5.0 2.5 - - + -
168B VAL* 1.3 77.8 - - - +
170B PHE* 1.3 64.5 + - - +
180B ILE* 2.9 18.9 - - - +
181B ASP* 3.1 17.2 + - - +
182B ALA* 3.1 33.6 + - + +
184B VAL* 6.6 0.2 - - + -
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Residues in contact with PHE 170 (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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4B LEU* 3.3 16.9 - - - +
5B PHE 3.0 22.1 + - - +
136B ALA* 4.4 5.6 - - + -
137B PRO* 3.3 39.0 - - + -
140B TYR* 3.4 30.3 - + + -
168B VAL* 3.6 21.1 - - + -
169B THR* 1.3 78.9 - - - +
171B GLN* 1.3 61.1 + - - +
172B TYR* 3.7 21.8 + - + -
177B ILE* 3.5 26.0 - - + -
179B GLY 3.4 4.0 - - - +
180B ILE* 4.0 14.8 - - + -
215B TRP* 3.6 30.1 - + - -
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Residues in contact with GLN 171 (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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2B LYS* 5.8 3.8 - - + -
4B LEU* 3.5 17.0 - - + -
170B PHE* 1.3 71.2 - - - +
172B TYR* 1.3 61.5 + - - +
177B ILE* 3.4 6.8 - - - +
178B VAL* 2.9 54.3 + - + +
179B GLY* 2.6 23.5 + - - +
180B ILE 3.6 9.1 + - - +
181B ASP* 2.6 42.9 + - - +
215B TRP 5.4 0.2 + - - -
217B THR* 5.4 6.5 + - - +
219B ALA* 5.2 7.9 - - - +
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Residues in contact with TYR 172 (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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1B ALA 3.4 3.3 - - - +
2B LYS* 3.2 4.5 - - - +
3B HIS* 2.8 68.5 + + + +
5B PHE* 4.1 23.6 - - + -
129B GLU* 2.6 40.4 + - - -
137B PRO* 3.4 17.4 - - + +
170B PHE* 3.7 27.8 - - + -
171B GLN* 1.3 77.2 - - - +
173B ASP* 1.3 58.2 + - - +
175B GLY 3.8 16.4 - - - -
176B LYS 3.3 15.9 - - - +
177B ILE* 3.7 17.7 - - + +
254B MET* 3.4 11.5 - - + +
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Residues in contact with ASP 173 (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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1B ALA 3.6 15.8 + - - -
2B LYS* 2.9 43.8 + - + +
172B TYR* 1.3 75.2 - - - +
174B ASP* 1.3 92.6 + - - +
175B GLY 2.9 4.9 - - - -
176B LYS* 2.9 20.9 + - - +
178B VAL* 3.5 21.2 - - + +
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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