Contacts of the strand formed by residues 49 - 57 (chain F) in PDB entry 6XAV
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 49 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F MET* 4.2 7.0 - - + +
2F ASN 6.1 0.2 - - - -
3F LEU* 6.0 1.1 - - - +
39F LEU* 3.3 59.7 - - + +
42F HIS* 4.7 9.2 - - + -
43F ALA* 3.8 9.9 - - + +
47F GLU 4.4 6.7 - - - +
48F ASP* 1.3 80.6 - - - +
50F PHE* 1.3 65.7 + - - +
100F LYS* 3.4 7.5 - - - +
101F ILE* 2.7 61.0 + - + +
103F PRO* 3.8 22.2 - - + -
111F PHE* 5.5 1.6 - - + -
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Residues in contact with PHE 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET 3.0 33.1 + - - +
2F ASN* 3.3 9.8 - - + +
3F LEU 3.3 14.9 + - - -
48F ASP* 4.0 30.3 - - + -
49F ILE* 1.3 78.0 - - - +
51F GLY* 1.3 59.5 + - - +
99F GLY* 3.5 5.4 - - - +
100F LYS* 3.8 27.8 - - + -
101F ILE* 3.8 8.2 - - - +
117F ASN* 3.5 27.1 - - - -
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Residues in contact with GLY 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ASN* 4.1 8.2 + - - -
3F LEU* 4.3 8.1 - - - -
50F PHE* 1.3 76.8 - - - +
52F ASP* 1.3 66.4 + - - +
65F LEU* 5.6 0.2 - - - +
79F ILE* 3.9 9.6 - - - -
98F SER* 3.2 20.6 - - - -
99F GLY 3.2 12.3 + - - -
101F ILE* 3.7 16.6 - - - +
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Residues in contact with ASP 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ASN* 2.9 35.2 + - - +
3F LEU* 4.9 8.9 - - - +
4F THR* 3.3 26.3 + - - +
51F GLY* 1.3 74.4 - - - +
53F GLY* 1.3 61.7 + - - +
65F LEU* 4.5 3.9 - - - +
66F ARG 4.8 0.2 - - - +
67F SER* 5.1 4.5 - - - -
79F ILE* 3.7 14.3 - - - +
96F THR* 5.1 6.0 - - + +
97F ILE 3.3 9.9 - - - +
98F SER* 3.7 17.3 - - - -
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Residues in contact with GLY 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ASP* 1.3 82.4 + - - +
54F VAL* 1.3 66.7 - - - -
65F LEU* 3.5 14.9 - - - +
66F ARG 3.2 13.7 - - - -
67F SER* 4.9 1.6 - - - -
68F ALA 5.7 0.4 - - - -
96F THR* 3.4 8.0 - - - +
97F ILE 3.2 27.1 + - - -
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Residues in contact with VAL 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F GLY* 1.3 72.7 - - - -
55F LEU* 1.3 64.8 + - - +
56F GLU 3.6 0.3 + - - -
64F PHE 3.3 0.2 - - - +
65F LEU* 3.9 0.4 - - - -
66F ARG* 2.6 41.6 + - - +
68F ALA* 5.8 2.5 - - + -
72F TYR* 3.5 33.9 - - + +
94F GLY* 3.7 27.8 - - - +
96F THR* 3.8 18.4 - - + +
245F MET* 3.7 23.6 - - + +
249F LYS* 4.0 21.1 - - + +
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F GLY 3.7 0.6 + - - -
54F VAL* 1.3 74.7 - - - +
56F GLU* 1.3 65.4 + - - +
57F ILE* 3.9 17.7 - - + -
63F GLY* 3.9 8.5 - - - -
64F PHE 3.4 17.3 - - - +
65F LEU* 3.7 7.9 - - + -
81F VAL* 3.8 28.9 - - + -
86F ILE* 4.8 2.9 - - + -
91F LEU* 3.7 33.2 - - + -
92F ARG 3.4 22.9 - - - +
93F THR* 3.6 3.0 - - - +
94F GLY 3.1 21.0 + - - -
95F ASP* 3.3 23.1 + - + +
97F ILE* 5.1 1.1 - - + -
245F MET* 3.3 10.1 - - - +
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Residues in contact with GLU 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU* 1.3 73.7 - - - +
57F ILE* 1.3 67.6 + - - +
58F LEU* 3.3 15.6 - - + +
63F GLY* 3.2 4.0 - - - -
64F PHE 2.7 25.5 + - - +
66F ARG* 2.5 53.9 + - + +
72F TYR 5.2 3.1 - - - +
93F THR* 4.5 3.1 - - + -
241F GLN* 3.0 45.8 + - - +
245F MET* 3.7 16.1 - - + +
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Residues in contact with ILE 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU* 3.9 17.7 - - + -
56F GLU* 1.3 73.4 - - - +
58F LEU* 1.3 76.0 + - - +
61F GLY* 3.8 19.7 - - - +
62F PHE 3.7 3.4 - - - -
63F GLY* 3.9 1.6 - - - -
86F ILE* 3.9 20.4 - - + -
91F LEU 3.7 24.0 - - - +
92F ARG* 3.8 16.2 - - - -
93F THR* 3.8 19.7 + - - +
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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