Contacts of the helix formed by residues 42 - 51 (chain B) in PDB entry 5C1V
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 ARG 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B LYS 3.1 24.7 + - - -
33B GLU 3.0 18.1 + - - +
34B VAL* 2.8 20.8 + - - +
35B PHE 3.2 16.9 + - - +
36B ASP* 3.2 31.0 - - + +
37B ASN 5.0 0.2 - - - +
40B LYS 4.9 0.2 - - - +
41B PRO* 1.3 69.2 - - - +
43B VAL* 1.3 64.5 + - - +
44B ASP* 3.3 18.2 + - - +
45B ILE* 3.4 21.6 + - + +
46B LEU* 3.1 21.4 + - - +
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Residues in contact with VAL 43 (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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41B PRO* 3.3 17.2 + - + +
42B ARG* 1.3 73.2 - - - +
44B ASP* 1.3 69.8 + - + +
46B LEU* 3.4 7.9 - - - +
47B LYS* 2.8 31.4 + - - +
132B TYR* 3.7 11.3 + - + +
135B ALA* 4.4 9.2 - - + +
136B LEU* 3.4 33.7 - - + -
139B LEU* 3.8 27.8 - - + -
140B TYR* 5.1 4.9 - - + +
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Residues in contact with ASP 44 (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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42B ARG* 3.8 18.5 - - - +
43B VAL* 1.3 83.3 + - + +
45B ILE* 1.3 77.5 + - + +
47B LYS* 3.8 8.7 - - - +
48B ALA* 3.3 22.2 + - - +
132B TYR* 5.6 0.4 - - - -
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Residues in contact with ILE 45 (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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24B PRO* 6.1 3.6 - - + -
29B LEU* 4.7 18.8 - - + -
33B GLU* 4.4 14.8 - - + +
34B VAL* 5.6 1.8 - - - -
42B ARG* 3.8 30.5 - - + +
43B VAL 3.4 0.2 - - - -
44B ASP* 1.3 89.5 + - + +
46B LEU* 1.3 64.9 + - - +
48B ALA* 3.4 5.8 + - - +
49B HIS* 3.2 22.3 + - + +
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Residues in contact with LEU 46 (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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29B LEU* 4.4 4.5 - - + -
34B VAL* 3.9 28.7 - - + -
41B PRO* 6.2 0.9 - - + -
42B ARG 3.1 15.2 + - - +
43B VAL* 3.4 12.8 - - - +
45B ILE* 1.3 76.0 - - - +
47B LYS* 1.3 66.4 + - - +
49B HIS* 3.4 2.3 + - - +
50B LEU* 3.0 46.4 + - + +
56B LEU* 4.2 30.5 - - + -
64B ILE* 4.7 4.0 - - + -
131B LEU* 5.0 4.0 - - + +
132B TYR* 3.7 26.0 - - + +
135B ALA* 4.8 10.3 - - + -
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Residues in contact with LYS 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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43B VAL 2.8 17.1 + - - +
44B ASP* 3.8 7.9 - - - +
46B LEU* 1.3 79.7 - - - +
48B ALA* 1.3 58.9 + - - +
50B LEU* 3.2 3.3 + - - +
51B MET* 3.0 53.2 + - - +
95B PHE* 4.6 1.7 - - - -
99B MET* 3.5 36.3 + - - +
103B GLU* 6.3 1.2 - - - +
132B TYR* 3.6 26.9 - - + +
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Residues in contact with ALA 48 (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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44B ASP 3.3 15.6 + - - +
45B ILE* 3.8 6.1 - - - +
46B LEU 3.2 0.6 - - - -
47B LYS* 1.3 82.2 - - - +
49B HIS* 1.3 58.5 + - - +
51B MET* 3.8 9.4 + - - +
52B LYS* 3.1 26.3 - - - +
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Residues in contact with HIS 49 (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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24B PRO* 4.0 21.6 + - + +
25B PRO* 3.3 22.5 + - + +
27B HIS 3.0 24.0 + - - -
29B LEU* 3.3 39.9 - - + +
45B ILE* 3.2 10.7 + - + +
46B LEU 3.7 7.0 - - - +
48B ALA* 1.3 78.0 - - - +
50B LEU* 1.3 61.6 + - - +
52B LYS* 3.1 14.4 + - - +
54B GLY* 2.9 33.9 + - - -
55B ARG 2.9 31.3 + - - -
56B LEU* 4.2 3.6 - - + -
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Residues in contact with LEU 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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46B LEU* 3.0 41.2 + - + +
47B LYS 3.8 3.6 - - - +
49B HIS* 1.3 76.6 - - + +
51B MET* 1.3 58.5 + - - +
52B LYS 3.0 4.9 - - - -
53B GLU* 3.0 19.8 + - - -
54B GLY 3.8 15.0 + - - +
55B ARG* 5.4 0.2 - - - -
56B LEU* 3.9 30.3 - - + -
95B PHE* 3.9 20.3 - - + -
125B PHE* 4.4 9.0 - - - -
128B GLU* 3.8 46.3 - - + +
131B LEU* 4.6 10.1 - - + -
132B TYR* 4.6 0.7 - - + -
170B TYR* 5.4 1.1 - - - +
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Residues in contact with MET 51 (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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47B LYS* 3.0 49.7 + - + +
48B ALA* 3.9 9.0 - - - +
49B HIS 3.3 0.4 - - - -
50B LEU* 1.3 73.2 - - - +
52B LYS* 1.3 64.8 + - + +
53B GLU 3.4 1.6 - - - -
95B PHE* 3.6 20.4 - - + -
96B PHE* 3.6 48.9 - - + -
99B MET* 3.8 17.9 - - + -
125B PHE* 5.8 0.6 - - - -
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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