Contacts of the strand formed by residues 3 - 10 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ALA* 4.2 6.2 + - - +
2C LYS* 1.3 81.0 - - - +
4C LEU* 1.3 73.3 + - - +
5C PHE* 4.5 6.4 - - + +
172C TYR* 2.7 75.8 + + + +
175C GLY* 5.3 8.1 - - - -
311D MET* 3.7 34.5 - - + +
312D VAL 5.6 2.9 - - - +
313D GLU* 6.2 0.2 - - - -
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Residues in contact with LEU 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LYS* 6.2 2.0 - - + -
3C HIS* 1.3 84.9 - - - +
5C PHE* 1.3 60.1 + - - +
6C THR 4.4 0.2 + - - -
169C THR* 4.5 6.7 - - - +
170C PHE 3.2 17.7 - - - +
171C GLN* 3.5 24.0 - - + -
181C ASP* 3.9 26.5 - - + +
297D GLN* 4.1 1.7 + - - -
308D THR 5.2 2.2 - - - +
309D SER* 4.8 21.4 + - - -
310D ILE 3.9 17.4 + - - +
311D MET* 2.9 36.8 - - - +
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Residues in contact with PHE 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C HIS* 4.2 8.6 + - + +
4C LEU* 1.3 73.6 - - - +
6C THR* 1.3 67.4 + - - +
7C SER* 3.3 22.9 - - - -
135C PRO* 6.3 0.2 - - + -
137C PRO* 3.9 19.7 - - + +
168C VAL 4.2 0.5 - - - +
169C THR* 3.3 1.4 - - - -
170C PHE* 3.0 33.6 + - - +
172C TYR* 4.1 19.5 - - + -
252C GLY 3.9 2.9 - - - -
253C GLY* 3.4 8.7 - - - -
254C MET* 3.2 47.8 - - + -
123D PHE* 4.1 2.9 - + - -
256D ARG* 3.2 31.2 - - - -
297D GLN* 3.7 19.5 - - - +
311D MET* 4.7 4.3 - - - -
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Residues in contact with THR 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 1.3 79.1 - - - +
7C SER* 1.3 66.1 + - - +
167C GLN* 3.6 18.2 - - + -
168C VAL 3.3 14.1 - - - +
169C THR* 3.2 18.6 - - + +
121D LEU* 2.8 28.6 - - + +
297D GLN* 3.1 12.3 + - - +
299D SER* 3.5 25.4 - - - +
309D SER* 2.5 34.6 + - - -
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Residues in contact with SER 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 3.3 14.3 + - - -
6C THR* 1.3 71.8 - - - +
8C GLU* 1.3 64.3 + - - +
137C PRO* 3.6 32.0 - - - +
138C ILE* 4.0 4.8 + - - -
141C ALA* 4.7 2.6 - - - +
167C GLN* 3.5 5.2 - - - +
168C VAL* 3.1 29.5 + - - +
251C TYR 4.5 0.7 + - - -
252C GLY* 2.6 35.8 + - - -
121D LEU* 4.1 5.2 - - - -
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Residues in contact with GLU 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C SER* 1.3 78.6 - - - +
9C SER* 1.3 66.2 + - - +
10C VAL* 5.1 3.0 - - - +
138C ILE* 3.6 10.1 - - - +
141C ALA* 3.9 6.2 - - - +
165C LYS* 4.2 11.3 + - - -
166C SER 3.2 13.0 - - - +
167C GLN* 4.3 6.1 - - - +
245C LYS* 5.2 6.7 + - - -
247C ILE* 6.3 1.8 - - + -
248C VAL* 3.6 30.6 - - + +
252C GLY* 4.9 1.7 + - - -
684C PPK 5.2 4.6 + - - -
119D GLN* 3.9 18.7 + - - +
120D GLY* 4.1 15.1 - - - -
121D LEU* 3.5 20.9 + - + +
258D GLY 3.6 18.3 - - - +
259D GLY* 5.2 2.4 - - - -
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Residues in contact with SER 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLU* 1.3 75.8 + - - +
10C VAL* 1.3 69.5 + - - +
138C ILE* 5.0 0.2 - - - -
141C ALA* 3.6 31.0 - - - -
142C HIS* 2.4 40.3 + - - -
145C VAL* 3.9 6.6 - - - +
165C LYS* 3.6 1.0 - - - +
166C SER* 2.8 31.3 + - - +
248C VAL* 4.2 6.9 - - - +
119D GLN* 4.3 1.0 + - - -
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Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLU* 5.1 3.4 - - - +
9C SER* 1.3 83.7 + - - +
11C SER* 1.3 64.6 + - - +
14C HIS* 3.7 21.3 - - + -
17C LYS* 3.7 30.2 - - + +
145C VAL* 3.6 13.1 - - - +
164C ALA 3.7 4.0 - - - +
165C LYS* 3.4 27.1 - - + -
245C LYS* 3.9 34.8 - - + -
248C VAL* 4.4 6.3 - - + +
357C 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
------------------------------------------------------------
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