Contacts of the strand formed by residues 4 - 9 (chain C) in PDB entry 2X1L
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 PRO 4 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER 3.8 4.7 - - - +
3C GLU* 1.3 112.5 - - - +
5C PHE* 1.3 60.4 + - - +
41C TYR* 4.5 1.7 - - - -
42C ASP* 3.2 14.1 - - + +
253C ARG* 3.4 45.8 - - + +
254C TYR* 4.1 13.7 - - + -
258C ASP* 4.0 10.3 - - - +
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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
----------------------------------------------------------
4C PRO* 1.3 75.3 - - - +
6C TYR* 1.3 58.8 + - - +
7C ILE* 3.6 35.4 - - + -
32C ILE* 4.0 17.7 - - + -
33C ALA* 4.9 0.9 - - - -
36C LYS* 3.7 49.6 - - + -
41C TYR* 4.1 16.6 - + + -
42C ASP 2.8 8.7 + - - -
43C VAL* 3.2 22.7 - - + -
44C ARG 2.9 25.7 + - - +
254C TYR* 4.7 1.5 - - - -
258C ASP* 3.5 30.5 - - + -
259C LEU* 4.7 9.0 - - + -
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Residues in contact with TYR 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO 4.3 0.2 - - - -
5C PHE* 1.3 71.9 - - - +
7C ILE* 1.3 63.2 + - - +
8C THR* 3.6 18.4 - - + +
44C ARG* 3.3 28.7 - - + -
46C LEU* 3.2 30.7 - - + +
237C TYR 2.7 30.3 + - - -
240C GLY* 4.2 1.7 - - - -
241C VAL* 3.6 24.8 - - + +
254C TYR* 3.5 34.7 - - + +
255C TRP* 3.9 13.0 - + - -
257C ALA* 3.5 30.2 - - + +
258C ASP* 2.9 37.0 + - - +
259C LEU 3.3 7.1 + - - +
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Residues in contact with ILE 7 (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* 3.6 17.9 + - + -
6C TYR* 1.3 74.1 - - - +
8C THR* 1.3 70.5 + - - +
29C THR* 3.7 24.7 - - + +
32C ILE* 3.8 33.2 - - + -
33C ALA* 4.0 24.7 - - + -
43C VAL* 4.6 1.1 - - + -
44C ARG 3.0 15.2 + - - +
45C TYR* 4.1 11.6 - - + -
46C LEU 3.0 23.6 + - - -
259C LEU* 3.5 30.5 - - + +
261C MET* 4.1 4.0 - - + -
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Residues in contact with THR 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 3.6 35.2 - - + +
7C ILE* 1.3 80.5 - - - +
9C THR* 1.3 64.0 + - - +
29C THR* 4.0 2.4 - - - +
46C LEU* 3.3 13.2 - - + -
237C TYR* 3.3 28.4 - - + -
257C ALA* 5.0 0.7 - - + -
259C LEU 3.1 5.2 + - - +
260C HIS* 2.7 34.5 + - + +
261C MET* 2.9 32.4 + - - +
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Residues in contact with THR 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C THR* 1.3 74.0 - - - +
10C ALA* 1.3 72.3 + - - +
11C ILE* 3.6 4.9 + - - +
25C GLU* 3.6 11.2 - - - +
26C TYR* 4.0 13.3 - - + -
29C THR* 3.5 36.3 - - + +
45C TYR* 3.9 13.7 - - + +
46C LEU 3.1 6.3 + - - +
47C THR* 2.6 31.9 + - - +
236C ASN* 5.1 0.2 - - - +
237C TYR* 3.4 21.5 - - - -
261C MET* 3.4 7.6 - - - -
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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
------------------------------------------------------------
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