Contacts of the helix formed by residues 46 - 56 (chain B) in PDB entry 3KDH
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 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B ALA* 1.3 92.4 - - + +
47B ALA* 1.3 65.1 + - - +
48B SER* 3.7 18.2 - - - +
49B VAL* 3.0 28.1 + - + +
50B VAL* 3.2 10.2 + - - +
132B GLU* 3.5 12.6 - - - +
141B VAL* 3.8 20.8 - - + -
143B THR* 4.1 0.2 - - - +
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PRO* 1.3 71.2 - - - +
48B SER* 1.3 56.1 + - - +
49B VAL 3.1 0.2 - - - -
50B VAL 4.3 0.9 - - - +
51B TRP* 2.8 35.2 + - - +
108B ARG* 3.6 31.9 - - - +
130B VAL* 4.0 16.8 - - + +
131B ASN 5.0 0.2 - - - -
132B GLU* 2.8 30.6 + - + +
143B THR* 3.1 14.3 + - - +
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 3.7 15.5 - - - +
47B ALA* 1.3 77.4 - - - +
49B VAL* 1.3 64.9 + - - +
51B TRP* 5.2 0.7 - - - -
52B PRO* 3.2 22.6 - - - +
108B ARG* 4.3 14.3 - - - +
132B GLU* 4.3 1.4 + - - -
186B MET* 4.1 6.9 - - - +
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA* 4.6 1.1 - - + -
46B PRO* 3.0 26.4 + - + +
48B SER* 1.3 89.7 - - - +
50B VAL* 1.3 65.5 + - - +
51B TRP 3.5 0.4 - - - -
52B PRO* 3.5 8.4 - - - +
53B LEU* 3.8 13.9 - - + +
180B ALA 5.4 0.2 - - - +
181B ALA* 3.5 33.0 - - + +
184B ALA 6.1 0.7 - - - +
186B MET* 4.2 37.2 - - + +
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE* 4.0 23.1 - - + -
45B ALA* 4.3 2.7 - - + -
46B PRO 3.2 13.0 + - - +
47B ALA 4.0 3.8 - - - +
49B VAL* 1.3 75.5 - - - +
51B TRP* 1.3 66.8 + - - +
53B LEU* 3.1 21.5 + - - +
54B ILE* 3.7 7.6 + - + +
130B VAL* 4.0 13.2 - - + -
143B THR* 3.9 13.7 - - + +
145B VAL* 3.8 27.6 - - + -
177B LEU* 4.1 12.8 - - + +
181B ALA* 3.7 23.8 - - + -
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Residues in contact with TRP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA 2.8 21.3 + - - +
48B SER* 5.2 0.7 - - - -
50B VAL* 1.3 74.2 - - - +
52B PRO* 1.3 66.9 - - + +
54B ILE* 3.0 21.5 + - + +
55B ARG* 2.8 50.1 + - + +
103B VAL* 4.6 1.1 - - + -
104B ASP 4.0 4.0 - - - -
105B ASP* 3.6 36.3 + - - +
108B ARG* 3.3 57.2 - - + +
109B VAL 3.5 30.7 - - - -
110B LEU* 4.0 11.0 - - + -
128B THR 4.9 0.7 - - - -
130B VAL* 3.8 17.9 - - + +
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Residues in contact with PRO 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B SER* 3.2 27.1 - - - +
49B VAL 3.5 10.8 - - - +
51B TRP* 1.3 99.7 - - + +
53B LEU* 1.3 60.4 + - + +
55B ARG* 4.2 7.4 - - + -
56B ARG* 3.1 27.2 + - - +
186B MET* 4.5 13.0 - - + -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B VAL* 3.8 19.5 - - + +
50B VAL 3.1 6.8 + - - +
52B PRO* 1.3 78.2 - - + +
54B ILE* 1.3 61.2 + - - +
56B ARG* 4.1 12.7 + - - +
59B ASN 4.7 5.5 - - - +
60B PRO* 5.6 0.2 - - - +
62B ARG* 3.3 57.3 - - + +
63B TYR* 3.9 17.3 - - + -
177B LEU* 3.6 26.5 - - + -
180B ALA* 4.1 9.9 - - + +
181B ALA* 3.8 31.2 - - + +
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 3.7 8.2 + - + +
51B TRP* 3.0 15.2 + - + +
53B LEU* 1.3 77.5 - - - +
55B ARG* 1.3 65.3 + - - +
56B ARG 3.2 5.8 + - - +
57B PHE* 4.4 2.6 + - - -
63B TYR* 4.2 26.5 + - + +
83B ARG* 5.6 2.1 + - - -
110B LEU* 3.5 37.9 - - + +
128B THR* 3.8 25.6 - - + -
130B VAL* 3.5 30.3 - - + -
145B VAL* 4.4 1.1 - - + -
177B LEU* 3.8 30.7 - - + -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TRP* 2.8 46.0 + - + +
52B PRO* 3.4 7.8 + - + +
54B ILE* 1.3 78.6 - - - +
56B ARG* 1.3 56.4 + - - +
57B PHE* 2.8 11.0 + - - +
77B GLY 2.9 21.2 + - - -
78B ASP* 3.0 30.5 + - - +
79B VAL 5.2 0.6 - - - +
100B LEU* 4.1 8.1 - - - +
103B VAL* 3.4 21.8 - - - +
105B ASP* 3.1 29.1 + - - +
110B LEU* 4.0 10.1 - - - +
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PRO 3.1 18.2 + - - +
53B LEU* 4.3 8.6 - - - +
54B ILE 3.2 5.2 - - - +
55B ARG* 1.3 72.5 - - - +
57B PHE* 1.3 65.1 + - - +
58B ASP* 3.0 35.5 + - - +
59B ASN* 3.0 32.8 + - + +
60B PRO* 4.3 1.0 - - - +
83B ARG* 5.0 0.9 + - - -
187B HIS* 5.1 12.9 - - + +
188B ASP* 4.0 10.7 + - - -
189B ASP 3.0 32.8 + - - +
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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