Contacts of the strand formed by residues 34 - 43 (chain C) in PDB entry 3NJ0
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 THR 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C GLU 4.2 3.1 + - - -
31C ASP* 2.9 41.1 + - + +
32C PRO* 4.8 0.2 - - - +
33C THR* 1.3 91.6 + - - +
35C CYS* 1.3 62.5 + - - +
36C THR* 4.2 13.7 - - - +
150C THR* 5.2 4.0 - - - -
151C VAL 3.3 13.5 - - - +
152C ASP* 3.1 24.2 - - - +
153C ILE* 3.6 12.7 - - - +
159C GLU* 4.2 7.4 - - - +
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Residues in contact with CYS 35 (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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34C THR* 1.3 74.4 - - - +
36C THR* 1.3 64.0 + - - +
149C TYR* 3.9 15.6 - - - -
150C THR* 3.2 4.5 - - - -
151C VAL* 2.7 38.7 + - + +
153C ILE* 4.0 15.7 - - + -
159C GLU* 4.2 13.5 - - + -
162C THR* 4.1 7.4 - - + -
163C LYS* 3.4 46.7 - - - -
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Residues in contact with THR 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PHE* 3.9 16.2 - - + +
29C GLU 4.3 10.1 - - - +
30C PRO* 6.0 0.4 - - + -
34C THR* 4.2 11.4 - - - +
35C CYS* 1.3 77.7 - - - +
37C SER* 1.3 65.8 + - - +
149C TYR* 3.2 12.3 - - - -
150C THR* 3.0 29.4 - - + -
159C GLU* 5.2 2.4 + - - -
163C LYS* 4.0 14.0 - - - +
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Residues in contact with SER 37 (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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28C PHE* 5.3 0.7 - - - -
36C THR* 1.3 80.4 + - - +
38C LEU* 1.3 62.8 + - - +
39C ILE* 4.0 4.0 - - - +
148C SER* 3.2 6.2 - - - -
149C TYR* 3.0 46.6 + - - -
163C LYS* 2.9 24.2 + - - +
167C ASP* 2.7 31.4 + - - -
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Residues in contact with LEU 38 (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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22C ILE* 4.0 40.2 - - + -
26C HIS* 4.1 12.1 - - + +
37C SER* 1.3 76.5 + - - +
39C ILE* 1.3 73.7 + - - +
40C THR* 4.3 10.3 + - + +
146C LEU* 4.1 12.8 - - + -
147C GLU 3.7 25.8 - - - +
148C SER* 3.7 13.5 - - - +
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Residues in contact with ILE 39 (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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37C SER* 4.0 1.3 - - - +
38C LEU* 1.3 80.1 - - - +
40C THR* 1.3 68.2 + - - +
145C VAL 3.9 0.3 - - - +
146C LEU* 3.5 3.5 - - - -
147C GLU 2.9 37.8 + - - +
149C TYR* 4.6 6.3 - - + -
167C ASP* 3.5 43.3 - - + +
170C VAL* 3.7 25.1 - - + -
171C LYS* 3.8 39.5 - - + +
174C LEU* 3.8 12.8 - - + +
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Residues in contact with THR 40 (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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9C GLY 3.9 23.4 + - - +
10C LEU* 4.2 27.2 - - + +
38C LEU* 4.3 13.0 + - + +
39C ILE* 1.3 80.2 - - - +
41C GLN* 1.3 63.9 + - - +
144C VAL* 4.8 0.7 - - - -
145C VAL 3.4 4.9 - - - -
146C LEU* 3.6 25.1 - - + -
171C LYS* 2.8 28.2 + - - +
174C LEU* 4.2 2.0 - - - -
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Residues in contact with GLN 41 (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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10C LEU* 6.5 0.2 - - - -
40C THR* 1.3 76.3 - - - +
42C ARG* 1.3 81.4 + - - +
43C ILE* 3.7 15.1 + - + +
143C THR 3.7 0.7 - - - +
144C VAL* 3.4 4.6 - - - +
145C VAL* 2.9 40.5 + - + +
171C LYS* 3.0 26.5 + - - +
174C LEU* 3.4 39.5 + - + +
175C GLN* 3.2 32.0 + - - +
178C GLY* 5.7 1.6 - - - -
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Residues in contact with ARG 42 (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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9C GLY 3.6 21.8 + - - -
10C LEU* 4.0 6.4 - - + +
11C THR* 4.4 8.3 - - - +
14C GLU* 2.8 39.2 + - - -
40C THR* 5.5 0.2 + - - -
41C GLN* 1.3 92.0 + - - +
43C ILE* 1.3 62.5 + - - +
44C HIS* 4.4 25.8 + - + +
142C TYR* 3.5 30.9 - - + -
143C THR 3.4 3.6 - - - +
144C VAL* 4.5 5.8 - - + +
171C LYS* 5.2 0.2 - - - +
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Residues in contact with ILE 43 (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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41C GLN* 3.8 18.6 - - + +
42C ARG* 1.3 81.7 - - - +
44C HIS* 1.3 63.1 + - - +
45C ALA* 2.9 10.2 + - + +
50C VAL* 4.0 24.2 - - + -
142C TYR* 3.4 2.4 - - - +
143C THR* 2.7 41.7 + - - +
145C VAL* 3.8 25.1 - - + -
177C LEU* 4.0 14.4 - - + -
178C GLY* 3.6 38.8 - - - +
181C ALA* 4.1 1.8 - - + -
182C THR* 3.9 14.8 - - + -
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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