Contacts of the strand formed by residues 73 - 83 (chain F) in PDB entry 2VPF
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 73 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70F PRO* 3.6 31.3 - - + +
71F THR 5.4 0.9 - - - -
72F GLU* 1.3 78.2 - - - +
74F SER* 1.3 60.9 + - - +
97F LEU* 3.5 34.9 - - + +
98F GLN 3.3 13.0 - - - +
99F HIS* 4.1 7.6 + - + -
100F ASN* 3.2 7.4 - - - +
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Residues in contact with SER 74 (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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73F GLU* 1.3 72.9 - - - +
75F ASN* 1.3 68.9 + - - +
97F LEU* 3.5 7.8 - - - +
98F GLN* 2.8 44.2 + - - +
100F ASN* 3.0 30.4 + - - -
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Residues in contact with ASN 75 (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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74F SER* 1.3 81.0 + - - +
76F ILE* 1.3 66.1 + - - +
77F THR* 5.8 0.7 - - - +
95F SER* 5.2 12.0 - - - +
96F PHE 3.4 10.9 + - - +
97F LEU* 3.2 30.2 - - - +
98F GLN* 5.0 2.2 - - - +
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Residues in contact with ILE 76 (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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13E GLU 4.9 5.6 - - - +
15E VAL* 3.8 22.9 - - + -
23E ARG* 5.9 0.9 - - - +
54F LEU* 3.8 18.4 - - + -
75F ASN* 1.3 77.3 - - - +
77F THR* 1.3 73.4 + - - +
78F MET* 4.0 15.0 - - + -
94F MET 3.8 1.0 - - - +
95F SER* 3.3 2.1 - - - -
96F PHE* 2.8 38.0 + - + +
98F GLN* 3.7 40.8 - - + +
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Residues in contact with THR 77 (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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13E GLU 4.1 2.4 + - - +
14E VAL* 3.5 29.4 - - + -
15E VAL* 3.0 24.4 + - - +
75F ASN* 5.8 0.9 - - - +
76F ILE* 1.3 76.4 - - - +
78F MET* 1.3 68.3 + - - +
93F GLU* 3.8 31.2 - - + +
94F MET 3.5 7.6 - - - +
95F SER* 3.6 15.6 + - - +
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Residues in contact with MET 78 (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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14E VAL* 4.3 3.4 - - - -
15E VAL* 3.6 21.3 - - + +
20E VAL* 4.0 19.5 - - + -
23E ARG* 4.8 6.3 - - - +
52F VAL* 3.9 28.9 - - - -
53F PRO* 3.6 29.2 - - + +
54F LEU* 4.2 2.7 - - + -
76F ILE* 4.0 31.9 - - + -
77F THR* 1.3 82.4 - - - +
79F GLN* 1.3 61.5 + - - +
80F ILE* 3.5 13.1 + - + +
93F GLU* 3.5 3.5 - - - -
94F MET 3.0 32.2 + - - +
96F PHE* 4.3 11.4 - - + -
98F GLN* 5.4 0.9 - - - +
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Residues in contact with GLN 79 (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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14E VAL* 3.8 15.4 - - + +
15E VAL 3.0 15.8 + - - +
16E LYS* 3.3 32.2 - - - +
17E PHE* 2.9 58.8 + - + +
20E VAL* 3.8 4.9 - - - +
78F MET* 1.3 70.0 - - - +
80F ILE* 1.3 65.3 + - - +
91F ILE* 4.7 10.7 - - + +
92F GLY 3.2 11.0 - - - +
93F GLU* 4.7 5.8 + - + +
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Residues in contact with ILE 80 (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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17E PHE* 4.7 0.4 - - - -
20E VAL* 4.1 12.6 - - + -
35F ILE* 3.9 19.7 - - + -
47F PHE* 4.1 5.4 - - + -
48F LYS 3.8 8.5 - - - +
49F PRO* 4.1 8.5 - - + -
52F VAL* 3.7 28.3 - - + -
78F MET* 3.9 13.5 - - + +
79F GLN* 1.3 82.9 - - - +
81F MET* 1.3 75.5 + - - +
82F ARG* 4.0 2.3 + - + +
91F ILE* 4.5 2.7 - - - -
92F GLY 2.9 30.3 + - - +
94F MET* 3.8 37.5 - - + +
96F PHE* 4.4 4.5 - - + -
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Residues in contact with MET 81 (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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17E PHE* 3.5 32.4 - - + -
47F PHE* 3.3 6.1 - - - -
48F LYS* 2.8 57.5 + - + +
80F ILE* 1.3 77.3 - - - +
82F ARG* 1.3 58.6 + - - +
83F ILE* 4.1 15.9 - - + -
89F GLN* 3.3 37.7 - - + +
90F HIS 3.3 11.2 - - - +
91F ILE* 3.5 39.0 - - + +
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Residues in contact with ARG 82 (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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39F TYR* 4.9 4.8 - - - -
42F GLU* 2.6 43.9 + - - +
45F TYR* 3.4 45.0 + - + -
46F ILE 3.5 1.8 - - - -
47F PHE* 3.1 35.9 - - + -
80F ILE 4.0 2.8 + - - +
81F MET* 1.3 72.0 - - - +
83F ILE* 1.3 62.1 + - - +
88F GLY 4.4 1.0 - - - +
89F GLN* 3.8 0.5 - - - -
90F HIS* 3.0 45.0 + - + +
92F GLY 6.3 0.2 - - - +
94F MET* 4.3 16.3 - - - +
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Residues in contact with ILE 83 (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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45F TYR* 3.4 7.5 - - - +
46F ILE* 2.7 67.4 + - + +
48F LYS* 3.9 30.7 - - + -
81F MET* 4.1 12.8 - - + -
82F ARG* 1.3 79.5 - - - +
84F LYS* 1.3 77.7 + - - +
85F PRO* 4.5 3.1 - - + -
86F HIS 5.4 0.4 - - - +
87F GLN 5.3 0.4 - - - +
88F GLY 4.9 11.4 - - - +
89F GLN* 4.0 18.6 - - + +
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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