Contacts of the helix formed by residues 67 - 80 (chain V) in PDB entry 5XS0
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 GLU 67 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167L LEU 4.5 1.9 - - - +
169L LYS* 3.0 39.7 + - - +
51V TYR 4.5 1.6 + - - -
53V SER* 3.8 13.4 + - - +
65V TYR* 3.8 26.7 + - + -
66V ILE* 1.3 77.4 - - - +
68V GLY* 1.3 67.2 + - - +
69V HIS* 2.8 35.1 + - + +
70V ARG* 3.0 33.8 + - + +
71V VAL* 3.1 11.5 + - - +
152V LYS* 5.3 0.2 - - - +
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Residues in contact with GLY 68 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167L LEU* 5.6 0.9 - - - -
66V ILE 3.8 1.4 + - - -
67V GLU* 1.3 72.7 - - - +
69V HIS* 1.3 63.3 + - - +
71V VAL* 3.0 6.4 + - - +
72V ILE* 2.9 31.6 + - - +
148V THR* 4.3 24.1 - - - +
152V LYS* 4.5 11.2 - - - +
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Residues in contact with HIS 69 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160L ASN* 5.9 0.6 + - - -
164L ASN* 3.2 38.6 + - - +
165L CYS* 5.9 0.2 - - - -
167L LEU* 3.7 36.4 + - + +
168L ASP* 3.8 32.6 + - - +
67V GLU* 2.8 34.7 + - + -
68V GLY* 1.3 75.9 - - - +
70V ARG* 1.3 85.9 + - + +
72V ILE* 4.2 3.1 - - - -
73V ASN* 2.9 40.7 + - - +
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Residues in contact with ARG 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L ASP* 4.0 18.2 + - - -
169L LYS* 5.8 2.4 - - - +
170L ASP* 4.1 11.9 + - - -
195U ASP* 4.9 0.9 - - - +
50V GLU 3.8 14.7 + - - -
51V TYR* 3.7 47.0 + - + +
52V ILE 5.4 0.2 + - - -
53V SER* 4.0 7.9 + - - -
66V ILE* 3.7 13.9 - - + -
67V GLU* 3.0 35.3 + - + +
69V HIS* 1.3 99.5 - - + +
71V VAL* 1.3 57.1 + - - +
73V ASN* 3.4 6.3 + - - +
74V LEU* 2.9 35.1 + - - +
184V LEU* 6.3 1.0 - - - +
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Residues in contact with VAL 71 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66V ILE* 3.7 25.1 - - + -
67V GLU 3.3 14.6 - - - +
68V GLY 3.0 6.1 + - - +
70V ARG* 1.3 73.2 - - - +
72V ILE* 1.3 61.9 + - + +
74V LEU* 3.3 8.7 + - + +
75V ALA* 2.9 28.8 + - - +
151V LEU* 5.8 2.2 - - + -
152V LYS* 4.0 32.3 - - + -
155V LEU* 3.8 31.2 - - + -
162V LEU* 4.3 16.3 - - + +
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Residues in contact with ILE 72 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156L ARG* 4.2 4.9 - - + +
157L SER* 3.8 36.3 - - - +
164L ASN* 3.5 27.8 - - - +
167L LEU* 5.7 3.4 - - + -
68V GLY 2.9 18.1 + - - +
69V HIS* 3.6 8.3 - - - +
70V ARG 3.3 0.2 - - - -
71V VAL* 1.3 77.4 - - + +
73V ASN* 1.3 56.3 + - - +
75V ALA* 3.3 6.3 + - - +
76V ASN* 2.9 50.1 + - - +
84V TRP* 4.4 9.6 - - + -
151V LEU* 4.4 22.2 - - + -
155V LEU* 5.5 0.2 - - - -
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Residues in contact with ASN 73 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L ARG* 5.7 1.6 + - - -
159L GLY* 4.7 0.6 - - - -
160L ASN* 2.9 40.7 + - - +
164L ASN* 3.0 24.1 + - - +
195U ASP* 3.6 22.2 - - + +
69V HIS* 2.9 23.0 + - - +
70V ARG* 3.8 5.9 - - - +
72V ILE* 1.3 72.9 - - - +
74V LEU* 1.3 66.5 + - - +
76V ASN* 3.3 11.7 + - - +
77V GLU* 2.9 31.9 + - + +
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Residues in contact with LEU 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192U LYS* 3.6 31.4 - - + -
195U ASP* 4.0 8.3 + - - +
47V LEU* 4.2 9.0 - - + -
51V TYR* 3.9 23.6 - - + -
66V ILE* 4.6 15.9 - - + -
70V ARG 2.9 26.1 + - - +
71V VAL* 3.5 12.8 - - - +
72V ILE 3.3 0.2 - - - -
73V ASN* 1.3 77.2 - - - +
75V ALA* 1.3 57.0 + - - +
77V GLU* 3.4 4.4 + - - +
78V MET* 2.9 35.6 + - + +
161V ALA* 3.6 23.3 - - + +
162V LEU* 3.7 17.7 - - + -
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Residues in contact with ALA 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71V VAL 2.9 16.5 + - - +
72V ILE 3.7 4.0 - - - +
74V LEU* 1.3 73.4 - - - +
76V ASN* 1.3 60.5 + - - +
78V MET* 4.4 0.2 - - - -
79V PHE* 2.9 43.0 + - + +
84V TRP* 3.7 28.8 - - + -
155V LEU* 3.8 21.1 - - + -
162V LEU* 3.7 10.3 - - + +
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Residues in contact with ASN 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L GLN* 3.2 13.8 + - - +
157L SER 3.3 22.2 + - - +
158L PHE* 3.6 19.0 + - - +
159L GLY* 3.6 7.6 - - - +
72V ILE* 2.9 31.1 + - - +
73V ASN* 3.3 10.0 + - - +
75V ALA* 1.3 75.8 - - - +
77V GLU* 1.3 62.8 + - + +
80V GLY* 2.9 28.4 + - - -
81V TYR* 3.5 18.0 - - - +
84V TRP* 3.0 20.0 + - - +
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Residues in contact with GLU 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L GLN* 4.6 6.4 + - - +
44L ARG* 2.6 55.1 + - - +
195U ASP* 3.5 41.5 - - + +
196U LEU* 3.8 15.9 - - - +
197U GLU* 4.5 10.0 + - + +
200U VAL* 4.4 4.0 - - - +
201U GLU* 5.5 1.7 + - - +
204U ARG* 3.3 14.7 + - - -
73V ASN* 2.9 24.0 + - + +
74V LEU* 3.9 3.4 - - - +
76V ASN* 1.3 82.2 - - + +
78V MET* 1.3 64.1 + - + +
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Residues in contact with MET 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192U LYS* 5.4 3.6 - - - -
195U ASP 6.1 0.2 - - - +
197U GLU* 4.1 13.5 - - + +
200U VAL* 3.4 13.2 - - + +
204U ARG* 2.7 17.2 + - - -
39V ILE* 3.6 50.5 - - + +
42V ALA* 3.8 27.8 - - + +
43V LEU* 3.6 28.7 - - + -
45V GLN* 5.3 0.4 - - - -
74V LEU* 2.9 26.9 + - + +
75V ALA* 3.9 3.1 - - - +
77V GLU* 1.3 78.2 - - + +
79V PHE* 1.3 70.4 + - + +
161V ALA* 4.6 6.5 - - + +
162V LEU* 4.6 5.8 - - + -
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Residues in contact with PHE 79 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81U TYR* 4.0 13.2 - + - -
204U ARG* 3.4 21.6 + - - +
31V TYR* 3.6 19.0 + - - +
35V GLU* 4.9 1.3 - - - +
39V ILE* 4.1 13.7 - - + -
43V LEU* 4.6 4.5 - - + -
75V ALA* 2.9 20.9 + - + +
78V MET* 1.3 87.4 - - + +
80V GLY* 1.3 60.1 + - - +
82V ASN* 5.0 0.5 - - - +
83V GLY* 3.2 33.7 - - - +
84V TRP* 3.9 15.9 - - + +
115V LEU* 3.6 33.0 - - + -
116V LYS* 5.3 2.4 + - - -
155V LEU* 4.7 4.0 - - + -
158V PHE* 4.3 11.0 - + + -
162V LEU* 3.5 33.2 - - + -
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Residues in contact with GLY 80 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L TYR* 4.3 6.7 - - - -
40L GLN* 3.3 13.2 - - - -
204U ARG* 3.5 9.6 - - - +
76V ASN* 2.9 20.5 + - - -
79V PHE* 1.3 77.2 - - - +
81V TYR* 1.3 67.3 + - - -
82V ASN* 3.0 5.1 + - - -
83V GLY 3.1 8.4 + - - -
84V TRP* 3.2 17.5 - - - -
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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