Contacts of the helix formed by residues 34 - 47 (chain A) in PDB entry 3KJR
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 ILE 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A TRP* 3.4 30.3 - - + +
32A PRO 3.3 11.6 + - - +
33A HIS* 1.3 74.1 + - - +
35A THR* 1.3 64.6 + - - +
37A ASP* 3.1 18.4 + - + +
38A PHE* 3.0 22.3 + - - +
146A LEU* 3.8 26.7 - - + -
174A THR* 4.3 5.6 - - + -
176A PHE* 3.9 12.1 - - + -
177A VAL* 4.3 11.0 - - + -
179A TYR* 3.2 44.4 - - + +
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A HIS* 3.6 23.1 + - - +
34A ILE* 1.3 74.5 - - - +
36A HIS* 1.3 72.6 + - + +
38A PHE* 3.4 9.7 + - - +
39A ARG* 3.3 53.8 + - - +
174A THR* 5.1 4.2 - - - +
179A TYR* 4.4 1.7 + - - -
513A NHE 5.8 1.6 - - - -
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Residues in contact with HIS 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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35A THR* 1.3 80.1 - - + +
37A ASP* 1.3 59.9 + - - +
39A ARG* 3.4 32.3 + - - +
40A PHE* 2.9 30.7 + - - +
172A PHE* 3.6 16.9 - + + -
179A TYR* 3.2 26.4 + - + +
181A PHE* 3.5 12.0 - - + -
513A NHE 3.1 34.6 + - - -
205B GLY 3.8 22.5 + - - +
206B THR* 4.2 19.4 - - + +
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL 5.7 0.2 - - - -
16A ALA* 3.8 16.1 - - - +
31A TRP* 5.2 4.0 + - - -
34A ILE* 3.1 30.9 + - + +
36A HIS* 1.3 74.0 - - - +
38A PHE* 1.3 66.8 + - - +
40A PHE* 3.6 2.9 - - - +
41A LEU* 3.1 27.2 + - - +
144A THR* 2.6 37.6 + - + -
181A PHE* 3.7 14.0 - - + -
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Residues in contact with PHE 38 (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 HIS* 3.4 37.9 - + + +
34A ILE 3.0 6.9 + - - +
35A THR 3.7 4.0 - - - +
36A HIS 3.3 0.2 - - - -
37A ASP* 1.3 78.2 + - - +
39A ARG* 1.3 71.2 + - + +
41A LEU* 4.0 6.7 - - + +
42A ARG* 3.2 41.8 + - + +
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Residues in contact with ARG 39 (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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35A THR* 3.3 40.3 + - - +
36A HIS* 3.4 29.5 + - - +
37A ASP 3.3 0.6 - - - -
38A PHE* 1.3 84.1 - - + +
40A PHE* 1.3 56.5 + - - +
42A ARG* 3.7 5.5 - - - +
43A ASN* 2.7 52.9 + - - +
205B GLY 5.9 1.6 - - - +
206B THR* 6.5 1.6 - - - +
207B ASP* 6.3 1.8 - - - +
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Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.7 23.5 - + - -
36A HIS 2.9 18.7 + - - +
37A ASP* 3.6 5.4 - - - +
39A ARG* 1.3 76.7 - - - +
41A LEU* 1.3 54.8 + - + +
43A ASN* 4.7 0.9 - - - +
44A GLY* 2.8 34.0 + - - -
142A TYR* 3.8 28.0 - + + -
144A THR* 4.4 6.3 - - - -
181A PHE* 3.6 48.2 - + + -
182A VAL 5.3 0.9 - - - -
202B LEU* 3.5 43.3 - - + +
203B MET* 3.7 26.2 - - - -
205B GLY* 4.9 4.5 + - - +
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Residues in contact with LEU 41 (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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14A PHE* 3.4 42.6 - - + +
37A ASP* 3.1 17.3 + - - +
38A PHE* 4.0 6.7 - - + +
40A PHE* 1.3 81.2 - - + +
42A ARG* 1.3 56.4 + - - +
45A THR* 2.8 48.5 + - + +
80A LEU* 5.9 4.5 - - + -
83A ARG* 5.4 2.2 - - - +
123A LEU* 3.9 22.9 - - + -
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Residues in contact with ARG 42 (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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38A PHE* 3.2 38.6 + - + +
39A ARG* 3.7 5.6 - - - +
41A LEU* 1.3 79.8 - - - +
43A ASN* 1.3 68.8 + - - +
45A THR* 3.6 0.2 + - - -
46A THR* 2.7 43.9 + - + +
82A ASN* 4.9 12.8 - - - +
83A ARG* 3.9 27.0 - - - +
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Residues in contact with ASN 43 (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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39A ARG* 2.7 39.7 + - - +
40A PHE* 5.0 0.6 - - - +
42A ARG* 1.3 90.3 + - - +
44A GLY* 1.3 63.5 + - - +
46A THR* 3.5 5.9 + - - -
47A TYR* 3.3 26.2 + - - +
198B PHE* 3.9 2.7 - - - -
202B LEU* 3.9 16.1 - - + +
206B THR 4.8 4.2 + - - -
207B ASP* 5.1 2.4 - - - +
208B ILE* 3.8 47.2 - - + +
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Residues in contact with GLY 44 (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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14A PHE* 3.7 22.3 - - - -
40A PHE 2.8 21.4 + - - -
43A ASN* 1.3 75.2 - - - +
45A THR* 1.3 59.7 + - - +
46A THR 3.7 0.2 + - - -
47A TYR* 4.1 9.5 + - - +
61A ASN* 4.9 0.2 + - - -
121A PHE* 3.6 15.6 - - - -
198B PHE* 4.3 4.4 - - - -
202B LEU* 3.8 17.0 - - - +
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Residues in contact with THR 45 (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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14A PHE* 3.8 29.6 - - + -
41A LEU* 2.8 32.6 + - + +
42A ARG 3.6 0.2 + - - -
44A GLY* 1.3 77.0 - - - +
46A THR* 1.3 58.7 + - - +
47A TYR 3.6 0.2 - - - -
61A ASN* 3.0 27.9 + - - +
63A VAL* 3.9 9.1 - - + +
83A ARG* 3.0 38.3 + - - +
121A PHE* 3.7 17.4 - - + -
123A LEU* 4.1 9.4 - - + +
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 2.7 30.9 + - + +
43A ASN* 3.5 7.3 + - - -
45A THR* 1.3 76.2 - - - +
47A TYR* 1.3 68.4 + - - +
48A ILE* 3.4 11.3 + - - +
61A ASN* 3.5 6.1 + - - +
81A LYS 4.2 4.9 - - - +
82A ASN* 4.3 20.0 - - + +
83A ARG* 3.3 40.4 - - + +
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Residues in contact with TYR 47 (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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43A ASN 3.3 9.7 + - - +
44A GLY 4.1 5.6 + - - +
45A THR 3.6 1.4 - - - -
46A THR* 1.3 77.3 + - - +
48A ILE* 1.3 71.0 + - - +
49A PRO* 3.4 38.3 - - + +
50A PRO* 3.4 15.0 - - + +
51A GLU* 5.1 0.2 + - - -
61A ASN* 2.8 22.0 + - - +
118A ASN* 4.0 4.0 + - - -
121A PHE* 5.7 0.7 - - - -
198B PHE* 3.3 74.9 + + + +
201B LEU* 5.9 1.1 - - + -
208B ILE* 5.3 3.6 - - + -
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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
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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