Contacts of the helix formed by residues 25 - 37 (chain A) in PDB entry 3JVX
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TRP* 4.0 14.8 + - + -
24A ARG* 1.3 74.9 - - - +
26A PRO* 1.3 67.8 - - - +
27A SER 3.2 2.2 - - - -
28A GLU* 3.1 26.2 + - + +
29A LEU* 3.1 22.7 + - + +
117A ILE* 3.7 32.5 - - + -
149A ASN* 3.4 34.5 - - + +
150A PRO* 3.8 12.3 - - + -
151A TYR* 3.9 16.6 - - + +
153A TYR* 3.7 31.4 - - + -
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Residues in contact with PRO 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.7 38.5 - - + +
25A LEU* 1.3 86.5 - - - +
27A SER* 1.3 54.4 + - - +
29A LEU* 3.3 7.9 + - + -
30A GLN* 2.5 46.6 + - + +
148A LYS* 3.4 27.4 - - + +
149A ASN* 3.2 15.3 - - - +
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PRO* 1.3 74.8 - - - +
28A GLU* 1.3 65.5 + - - +
30A GLN* 3.3 10.3 + - - +
31A TYR* 3.1 17.5 + - - +
144A LEU* 3.7 19.4 + - - +
149A ASN* 2.9 26.1 + - - +
153A TYR* 3.5 14.3 + - - -
155A TYR* 3.4 9.2 + - - -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA* 4.0 5.7 - - + +
23A TRP* 5.2 1.3 + - - +
25A LEU* 3.1 28.6 + - + +
27A SER* 1.3 75.3 - - - +
29A LEU* 1.3 61.1 + - + +
31A TYR* 3.3 4.5 + - - +
32A VAL* 3.0 31.7 + - - +
115A THR* 2.6 44.5 + - + -
153A TYR* 3.9 11.0 + - + -
155A TYR* 3.3 17.7 + - + -
208A EKB 2.8 46.3 + - - +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 5.1 4.9 - - + -
23A TRP* 6.1 0.9 - - + +
24A ARG* 6.4 0.4 - - + -
25A LEU* 3.1 30.9 + - + +
26A PRO* 3.3 11.9 + - + +
28A GLU* 1.3 77.0 - - + +
30A GLN* 1.3 69.0 + - - +
32A VAL* 3.2 9.4 + - + +
33A LYS* 2.9 29.1 + - - +
208A EKB 3.8 71.8 - - + +
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PRO* 2.5 42.8 + - - +
27A SER* 3.6 9.6 - - - +
28A GLU 3.3 0.2 - - - -
29A LEU* 1.3 87.2 - - - +
31A TYR* 1.3 58.5 + - - +
33A LYS* 3.4 16.5 + - - +
34A LYS* 3.0 32.0 + - - +
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Residues in contact with TYR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MET* 4.3 16.2 - - + -
27A SER 3.1 7.0 + - - +
28A GLU* 3.3 14.6 + - - +
30A GLN* 1.3 76.8 - - - +
32A VAL* 1.3 60.7 + - + +
34A LYS* 3.9 27.5 - - - +
35A THR* 2.7 54.3 + - + +
113A TYR* 3.9 23.7 - - + +
114A ILE 6.5 0.2 - - - -
115A THR* 4.5 4.7 - - - -
139A PHE* 4.7 11.0 - + - -
155A TYR* 3.4 65.6 - + + +
156A HIS 4.9 1.6 + - - -
157A VAL* 3.9 13.3 - - - +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MET* 4.0 14.4 - - + -
28A GLU* 3.0 23.4 + - - +
29A LEU* 3.4 11.0 - - + +
31A TYR* 1.3 77.0 - - + +
33A LYS* 1.3 59.3 + - - +
35A THR* 3.3 1.0 + - - -
36A THR* 2.7 38.7 + - - +
58A ARG* 5.3 1.6 - - - +
96A PHE* 3.4 37.5 - - + -
208A EKB 3.4 46.0 - - + +
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU 2.9 19.0 + - - +
30A GLN* 3.7 18.2 - - - +
32A VAL* 1.3 73.0 - - - +
34A LYS* 1.3 59.1 + - - +
36A THR* 3.5 0.2 + - - -
37A MET* 2.9 62.8 + - + +
56A PRO* 5.2 9.2 - - - -
58A ARG* 3.8 21.3 + - - +
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLN 3.0 18.2 + - - +
31A TYR* 4.0 29.6 - - - +
33A LYS* 1.3 79.0 - - - +
35A THR* 1.3 65.6 + - - +
36A THR 3.7 0.2 + - - -
37A MET* 4.0 12.4 + - - +
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A MET* 3.9 16.8 - - + -
31A TYR* 2.7 41.3 + - + +
32A VAL 4.0 0.7 - - - -
33A LYS 3.3 0.2 - - - -
34A LYS* 1.3 84.4 - - - +
36A THR* 1.3 61.4 + - - +
37A MET 3.8 1.1 + - - +
39A HIS* 4.3 6.4 - - - -
94A PHE* 3.6 14.0 - - + -
113A TYR* 3.6 39.9 - - + +
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MET* 4.2 20.0 - - + -
32A VAL* 2.7 29.0 + - + +
35A THR* 1.3 76.8 - - - +
37A MET* 1.3 69.5 + - - +
38A GLY 3.3 0.2 + - - -
39A HIS* 3.0 22.8 + - - +
41A LEU* 3.6 22.3 - - + +
58A ARG* 2.9 31.3 + - - +
94A PHE* 3.8 33.7 - - + -
96A PHE* 4.6 0.9 - - + -
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Residues in contact with MET 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LYS* 2.9 64.6 + - + +
34A LYS* 4.1 10.3 - - - +
35A THR 3.5 2.0 - - - +
36A THR* 1.3 79.4 + - - +
38A GLY* 1.3 60.1 + - - +
39A HIS* 3.5 10.4 + - - -
56A PRO* 3.6 27.4 - - + +
57A GLY* 3.7 20.4 - - - +
58A ARG* 3.8 8.7 - - - +
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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