Contacts of the strand formed by residues 160 - 173 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D GLN* 3.5 39.0 - - + +
151D VAL* 3.6 17.3 - - + -
152D ARG* 3.5 25.1 - - + +
157D LEU* 3.0 33.1 + - + +
158D PRO 3.8 6.2 - - - +
159D TRP* 1.3 110.7 - - + +
161D ARG* 1.3 63.5 + - - +
162D PRO* 4.8 0.3 - - - +
187D THR* 3.7 24.0 - - + +
188D GLN 3.9 1.6 - - - +
202D VAL* 5.3 1.1 - - + -
206D ILE* 4.3 4.3 - - + -
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Residues in contact with ARG 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ASP* 3.3 46.0 + - - +
82D MET* 3.8 26.2 - - + +
148D GLN* 3.1 17.7 + - - -
152D ARG* 3.6 4.0 - - - -
159D TRP* 4.3 1.6 + - - +
160D LEU* 1.3 78.0 + - - +
162D PRO* 1.3 79.1 - - + +
163D ASP 3.3 5.0 + - - +
188D GLN* 3.0 43.3 + - + +
189D HIS 3.6 31.1 + - - -
190D SER* 3.7 22.3 - - - +
191D GLU 4.9 0.8 - - - +
231D VAL* 4.8 8.1 + - - +
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Residues in contact with PRO 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D SER* 2.7 28.9 + - - -
13D GLY* 3.5 12.9 - - - -
75D ILE* 4.3 3.8 - - + -
76D GLY* 3.8 31.9 - - - +
77D TYR* 3.6 31.4 - - + +
82D MET* 4.3 8.3 - - - -
148D GLN* 4.0 1.4 + - - -
152D ARG* 3.4 31.4 + - - +
161D ARG* 1.3 95.2 - - + +
163D ASP* 1.3 54.3 + - - +
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Residues in contact with ASP 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885C SAM 2.6 38.1 + - - -
13D GLY 3.6 11.0 - - - +
14D HIS* 3.5 15.2 - - - +
15D PRO* 3.8 4.9 - - - +
77D TYR* 3.2 10.8 + - - +
161D ARG 3.3 2.8 + - - +
162D PRO* 1.3 78.7 - - - +
164D ALA* 1.3 62.0 + - - +
188D GLN* 2.7 55.2 + - + +
230D PHE* 3.6 7.0 - - - -
233D GLY* 3.6 1.4 - - - -
234D GLY* 2.8 22.5 + - - +
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885C SAM 4.7 0.2 - - - -
10D VAL* 3.7 1.0 - - - +
11D SER* 2.8 41.7 + - - -
14D HIS* 4.5 0.9 - - - +
145D VAL* 4.5 3.4 - - + -
148D GLN* 3.7 32.8 - - + +
163D ASP* 1.3 83.6 + - - +
165D LYS* 1.3 65.3 + - - +
185D LEU* 5.5 1.6 - - + -
186D SER 3.1 14.4 - - - +
187D THR* 3.8 5.6 - - - +
230D PHE* 4.8 2.7 - - - -
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Residues in contact with LYS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ASP* 3.0 23.1 + - - -
119C GLN* 3.6 34.1 + - - +
885C SAM 3.6 24.7 - - - +
887C MG 4.1 2.8 - - - -
8D GLU* 4.2 7.3 + - - -
9D SER 3.6 5.2 - - - +
10D VAL* 3.4 21.5 - - + +
14D HIS* 3.7 9.0 - - + -
145D VAL* 4.0 3.4 - - - -
164D ALA* 1.3 79.6 - - - +
166D SER* 1.3 62.2 + - - +
185D LEU* 3.6 3.9 - - - +
186D SER* 2.7 40.9 + - - +
230D PHE* 5.5 0.2 - - - -
245D LYS* 5.2 0.2 - - - +
884D PPK 2.7 38.9 + - - +
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Residues in contact with SER 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLN* 3.1 10.2 + - - +
8D GLU* 3.2 1.7 - - - -
9D SER 2.8 35.5 + - - -
141D ALA* 3.0 30.8 + - - +
144D LEU* 3.9 10.5 - - - -
145D VAL* 3.6 15.2 - - - +
165D LYS* 1.3 75.8 - - - +
167D GLN* 1.3 57.6 + - - +
184D VAL 3.4 4.7 - - - -
185D LEU* 3.8 19.7 - - - -
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Residues in contact with GLN 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLN* 3.3 16.3 + - - +
120C GLY* 2.5 37.0 + - - -
121C LEU* 4.8 0.6 - - - +
299C SER* 3.7 5.5 + - - -
300C TYR 2.7 28.8 + - - +
308C THR* 3.3 20.8 + - - -
6D THR* 3.6 12.5 - - + +
7D SER 3.4 14.4 - - - +
8D GLU* 4.1 4.4 - - + +
141D ALA* 5.5 0.2 - - - -
166D SER* 1.3 71.6 - - - +
168D VAL* 1.3 69.8 + - - +
169D THR* 5.1 2.4 - - + +
182D ALA 4.8 0.2 - - - -
183D VAL* 3.5 0.7 - - - -
184D VAL* 2.5 58.5 + - + +
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Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE 4.2 0.5 - - - +
6D THR* 3.4 0.9 - - - +
7D SER* 3.2 31.6 + - - +
137D PRO 5.2 1.3 - - - +
140D TYR 5.1 1.1 - - - -
141D ALA* 4.5 16.5 - - + +
144D LEU* 3.4 32.1 - - + -
167D GLN* 1.3 81.0 - - - +
169D THR* 1.3 66.8 + - - +
170D PHE* 3.6 27.6 + - + -
180D ILE* 3.4 30.7 - - + -
182D ALA 3.7 4.9 - - - +
183D VAL* 4.4 8.3 - - + -
211D LEU* 5.0 4.7 - - + -
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Residues in contact with THR 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C SER* 4.4 2.2 - - - +
308C THR* 4.3 12.5 + - - +
309C SER* 4.3 8.3 - - - -
4D LEU* 4.4 5.2 - - - +
5D PHE 3.4 6.3 - - - -
6D THR* 3.2 32.1 - - + +
167D GLN* 5.1 2.7 - - + -
168D VAL* 1.3 78.1 - - - +
170D PHE* 1.3 64.4 + - - +
180D ILE* 3.0 18.9 - - - +
181D ASP* 3.2 17.2 + - - +
182D ALA* 3.1 36.2 + - + +
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Residues in contact with PHE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.2 17.2 - - - +
5D PHE 3.0 21.4 + - - +
136D ALA* 4.4 5.6 - - + -
137D PRO* 3.3 39.9 - - + -
140D TYR* 3.5 30.1 - + + -
168D VAL* 3.6 21.5 - - + -
169D THR* 1.3 78.2 - - - +
171D GLN* 1.3 62.7 + - - +
172D TYR* 3.7 21.0 - - + -
177D ILE* 3.4 26.5 - - + -
179D GLY 3.4 3.4 - - - +
180D ILE* 4.0 15.0 - - + +
215D TRP* 3.5 30.1 - + - -
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Residues in contact with GLN 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LYS* 5.8 4.4 - - + +
4D LEU* 3.5 16.4 - - + -
170D PHE* 1.3 72.9 - - - +
172D TYR* 1.3 61.7 + - - +
177D ILE* 3.4 7.3 - - - +
178D VAL* 3.0 51.7 + - + +
179D GLY* 2.6 22.5 + - - +
180D ILE 3.7 7.3 + - - +
181D ASP* 2.5 43.0 + - - +
217D THR* 5.4 6.3 + - - +
219D ALA* 5.2 8.5 - - - +
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Residues in contact with TYR 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ALA 3.4 3.0 - - - +
2D LYS* 3.1 4.2 - - - +
3D HIS* 2.8 68.7 + + + +
5D PHE* 4.1 25.6 - - + -
129D GLU* 2.6 40.9 + - - -
137D PRO* 3.4 12.5 - - + +
170D PHE* 3.7 25.6 - - + -
171D GLN* 1.3 75.5 - - - +
173D ASP* 1.3 60.5 + - - +
175D GLY 3.9 15.9 - - - -
176D LYS 3.3 17.0 - - - +
177D ILE* 3.8 16.7 - - + +
254D MET* 3.3 17.9 - - + +
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Residues in contact with ASP 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ALA 3.5 16.6 + - - +
2D LYS* 2.9 43.3 + - + +
172D TYR* 1.3 74.3 - - - +
174D ASP* 1.3 86.7 + - - +
175D GLY 2.9 4.5 - - - -
176D LYS* 2.8 28.3 + - - +
178D VAL* 3.5 21.6 - - + +
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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