Contacts of the helix formed by residues 53 - 62 (chain B) in PDB entry 4XCS
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 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A CYS* 3.8 10.5 - - - -
175A ALA 3.9 20.0 - - - +
176A GLY* 4.3 5.8 - - - -
51B VAL 3.6 7.4 - - - +
52B CYS* 1.4 82.4 - - - +
54B THR* 1.3 61.2 + - + +
56B ILE* 3.1 8.0 + - + +
57B ILE* 2.9 42.5 + - + +
87B TRP* 3.7 24.0 - - + -
95B GLY* 3.7 25.1 - - - +
96B GLY 3.9 5.4 - - - +
97B LEU* 3.9 4.7 - - + +
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Residues in contact with THR 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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174A PRO* 5.8 1.4 - - - +
175A ALA* 4.0 25.3 - - + +
52B CYS* 3.0 21.9 + - - -
53B PRO* 1.3 79.3 - - + +
55B GLU* 1.3 55.7 + - - +
56B ILE 3.2 0.2 - - - -
57B ILE* 4.0 21.3 - - + -
58B ALA* 2.8 32.1 + - - +
23C ASP* 4.5 29.4 + - + -
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Residues in contact with GLU 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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42B PHE* 4.3 13.3 - - - -
44B TYR* 4.0 12.8 - - - +
51B VAL* 3.8 19.5 - - + +
52B CYS* 3.0 15.9 + - + +
54B THR* 1.3 78.3 + - - +
56B ILE* 1.3 60.4 + - - +
58B ALA* 4.3 3.4 - - - -
59B PHE* 3.2 22.3 - - + -
128B ARG* 4.5 7.6 - - - +
149B VAL 4.3 2.4 - - - +
150B GLY* 3.6 15.7 - - - -
151B ARG* 2.5 70.7 + - + +
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Residues in contact with ILE 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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42B PHE* 4.1 14.8 - - + -
44B TYR* 3.6 46.2 - - + +
51B VAL* 4.0 11.0 - - + -
52B CYS 4.7 0.4 - - - +
53B PRO 3.1 7.0 + - - +
55B GLU* 1.3 80.5 - - - +
57B ILE* 1.3 66.2 + - - +
58B ALA 3.2 1.7 + - - -
59B PHE* 3.2 4.5 + - - +
60B SER* 3.0 19.6 + - - -
87B TRP* 3.9 21.8 - - + -
97B LEU* 3.9 12.8 - - + -
100B MET* 3.7 25.4 - - - -
102B ILE* 4.5 5.7 - - + +
104B LEU* 4.2 15.5 - - + -
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Residues in contact with ILE 57 (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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53B PRO* 2.9 32.1 + - + +
54B THR* 4.0 19.5 - - + +
56B ILE* 1.3 76.5 - - - +
58B ALA* 1.3 58.7 + - - +
60B SER* 3.3 6.3 + - - -
61B ASP* 2.9 50.8 + - - +
92B LYS* 4.1 31.9 - - + +
96B GLY 3.8 21.1 - - - +
97B LEU* 3.7 21.1 - - + +
100B MET* 4.3 4.7 - - + -
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Residues in contact with ALA 58 (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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54B THR* 2.8 19.5 + - - +
55B GLU* 5.1 3.1 - - - -
56B ILE 3.2 0.4 - - - -
57B ILE* 1.3 78.0 - - - +
59B PHE* 1.3 60.7 + - + +
61B ASP* 3.9 5.6 - - - +
62B ARG* 3.4 32.2 + - - +
151B ARG 5.7 2.7 - - - +
153B VAL* 3.6 19.6 - - + +
23C ASP* 4.5 16.2 - - - +
25C GLN* 6.3 1.3 - - + -
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Residues in contact with PHE 59 (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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40B VAL* 4.5 9.9 - - + -
42B PHE* 4.4 19.1 - + + -
55B GLU* 3.2 25.6 - - + +
56B ILE 3.2 5.8 + - - +
57B ILE 3.2 0.2 - - - -
58B ALA* 1.3 78.4 - - + +
60B SER* 1.3 65.1 + - - +
62B ARG* 3.4 2.8 + - - -
63B ALA* 3.1 23.7 + - - +
66B PHE* 3.8 35.7 - + - -
73B VAL* 4.1 15.7 - - + +
102B ILE* 4.2 16.7 - - + +
130B LEU* 5.7 1.6 - - + -
151B ARG* 4.0 30.1 - - + -
153B VAL* 3.8 21.1 - - + -
156B THR* 3.7 28.5 - - + -
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Residues in contact with SER 60 (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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56B ILE 3.0 8.5 + - - -
57B ILE 3.6 7.4 - - - -
59B PHE* 1.3 74.5 - - - +
61B ASP* 1.3 63.1 + - - +
63B ALA* 3.2 9.5 + - - +
99B PRO 3.9 2.6 + - - -
100B MET* 3.4 33.4 - - - +
101B ASN* 2.7 55.5 + - - +
102B ILE* 4.1 15.5 - - - +
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Residues in contact with ASP 61 (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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57B ILE* 2.9 39.5 + - - +
58B ALA* 3.9 8.1 - - - +
60B SER* 1.3 79.3 + - - +
62B ARG* 1.3 66.4 + - + +
63B ALA 3.3 0.9 + - - -
64B GLU* 5.0 1.6 + - - +
92B LYS* 4.3 11.6 + - - -
100B MET* 6.0 0.2 - - - +
101B ASN* 4.2 7.0 - - - +
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Residues in contact with ARG 62 (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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58B ALA* 3.4 22.6 + - - +
59B PHE 3.6 2.7 - - - -
60B SER 3.2 0.2 - - - -
61B ASP* 1.3 85.9 - - + +
63B ALA* 1.3 64.0 + - - +
64B GLU 3.0 4.9 + - - -
65B GLU* 2.9 58.6 + - - +
66B PHE* 3.5 12.1 - - + -
153B VAL* 3.6 29.5 - - + +
154B ASP* 2.8 34.4 + - - +
157B LEU* 3.4 13.9 - - - +
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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