Contacts of the strand formed by residues 3 - 10 (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 HIS 3 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311C MET* 3.6 35.8 - - + +
312C VAL 5.5 2.2 - - - +
1D ALA* 4.3 5.6 + - - +
2D LYS* 1.3 81.4 - - - +
4D LEU* 1.3 74.2 + - - +
5D PHE* 4.4 6.6 - - + +
172D TYR* 2.8 73.3 + + + +
175D GLY* 5.3 7.9 - - - -
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Residues in contact with LEU 4 (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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297C GLN* 3.9 2.4 + - - -
308C THR 5.1 2.0 - - - +
309C SER* 4.7 22.6 + - - -
310C ILE 4.1 15.6 + - - +
311C MET* 3.0 32.1 - - - +
2D LYS* 6.2 2.0 - - + -
3D HIS* 1.3 80.8 - - - +
5D PHE* 1.3 61.2 + - - +
169D THR* 4.4 6.7 - - - +
170D PHE 3.2 17.7 - - - +
171D GLN* 3.5 28.3 - - + -
172D TYR 4.5 0.2 - - - +
181D ASP* 4.0 26.2 - - + +
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Residues in contact with PHE 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C PHE* 4.1 9.0 - + - -
256C ARG* 3.3 29.4 - - - -
297C GLN* 3.7 13.0 - - - +
311C MET* 4.9 4.0 - - - -
3D HIS* 4.2 9.1 + - + +
4D LEU* 1.3 73.6 - - - +
6D THR* 1.3 68.2 + - - +
7D SER* 3.3 22.7 - - - -
137D PRO* 3.9 19.7 - - + +
168D VAL 4.2 0.5 - - - +
169D THR* 3.4 1.5 - - - -
170D PHE* 3.0 32.4 + - - +
172D TYR* 4.1 19.2 - - + -
252D GLY 3.9 3.1 - - - -
253D GLY* 3.4 10.1 - - - -
254D MET* 3.2 48.0 - - + -
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Residues in contact with THR 6 (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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121C LEU* 2.8 27.7 - - + +
297C GLN* 3.2 11.7 + - - +
299C SER* 3.6 23.3 - - - -
309C SER* 2.6 34.6 + - - -
5D PHE* 1.3 80.0 - - - +
7D SER* 1.3 67.3 + - - +
167D GLN* 3.6 19.5 - - + -
168D VAL 3.4 13.5 - - - +
169D THR* 3.2 19.6 - - + -
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Residues in contact with SER 7 (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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121C LEU* 4.0 5.8 - - - -
5D PHE* 3.3 15.1 - - - -
6D THR* 1.3 68.6 - - - +
8D GLU* 1.3 65.5 + - - +
137D PRO* 3.6 25.6 - - - +
138D ILE* 4.0 11.8 + - - -
141D ALA* 4.8 2.2 - - - -
167D GLN* 3.4 6.1 - - - +
168D VAL* 3.2 28.8 + - - +
251D TYR 4.5 0.3 + - - -
252D GLY* 2.6 34.1 + - - -
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Residues in contact with GLU 8 (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* 3.9 21.0 + - - +
120C GLY* 4.2 10.1 - - - -
121C LEU* 3.6 18.2 + - + +
258C GLY 3.7 17.2 - - - +
259C GLY* 5.3 2.8 - - - +
7D SER* 1.3 77.3 - - - +
9D SER* 1.3 65.8 + - - +
10D VAL* 5.2 2.2 - - - +
138D ILE* 3.7 9.9 - - - +
141D ALA* 3.9 6.2 - - - +
165D LYS* 4.2 16.5 + - - -
166D SER 3.2 12.8 - - - +
167D GLN* 4.1 7.9 - - - +
245D LYS* 5.3 5.5 + - - -
247D ILE* 6.4 0.9 - - + -
248D VAL* 3.5 30.4 - - + +
252D GLY* 4.9 2.1 + - - -
884D PPK 5.1 6.6 + - - -
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Residues in contact with SER 9 (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* 4.5 1.4 + - - -
8D GLU* 1.3 76.8 - - - +
10D VAL* 1.3 70.0 + - - +
138D ILE* 4.9 0.2 - - - -
141D ALA* 3.6 31.9 - - - -
142D HIS* 2.4 40.7 + - - -
145D VAL* 3.9 5.6 - - - +
165D LYS* 3.6 0.7 - - - +
166D SER* 2.8 31.1 + - - +
248D VAL* 4.1 7.0 - - - +
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Residues in contact with VAL 10 (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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8D GLU* 5.2 2.9 - - - +
9D SER* 1.3 82.1 + - - +
11D SER* 1.3 64.8 + - - +
14D HIS* 3.7 22.9 - - + -
17D LYS* 3.7 30.8 - - + +
142D HIS* 5.9 0.2 - - - -
145D VAL* 3.6 14.0 - - - +
164D ALA 3.7 4.0 - - - +
165D LYS* 3.4 31.6 - - + -
245D LYS* 3.9 33.9 - - + -
248D VAL* 4.4 5.0 - - + +
357D TYR* 4.2 9.7 + - - -
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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