Contacts of the strand formed by residues 47 - 55 (chain P) in PDB entry 1VF5
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 LYS 47 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P GLU 3.8 3.5 - - - +
36P VAL* 4.0 0.3 - - - -
37P PRO* 3.5 16.8 - - + +
46P PHE* 1.3 91.1 - - - +
48P ALA* 1.3 65.2 + - - +
49P VAL* 3.5 29.6 - - + +
94P LEU 4.4 13.2 + - - -
95P LYS* 4.8 11.9 - - + +
98P VAL* 3.9 24.0 - - - +
128P VAL* 3.6 22.4 - - + +
129P PHE 3.6 2.9 - - - -
130P PRO* 5.1 0.4 - - - -
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Residues in contact with ALA 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P VAL* 5.6 0.9 - - + -
35P GLU 3.4 8.3 - - - -
36P VAL* 3.9 17.0 - - + -
46P PHE* 4.7 0.2 - - + -
47P LYS* 1.3 76.7 - - - +
49P VAL* 1.3 62.5 + - - +
50P VAL* 4.5 1.4 - - - +
76P LEU* 4.8 10.3 - - + -
78P LEU* 5.4 2.9 - - + -
129P PHE* 3.0 49.6 + - + +
131P VAL* 3.8 18.4 - - + -
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Residues in contact with VAL 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P GLU 3.5 1.2 - - - +
34P VAL* 3.4 4.4 - - - -
35P GLU* 2.9 41.1 + - + +
47P LYS* 3.5 33.0 - - + -
48P ALA* 1.3 70.8 - - - +
50P VAL* 1.3 61.0 + - - +
51P LYS* 3.5 31.6 + - + +
126P GLU* 3.4 35.4 - - + +
127P ILE 3.7 3.8 - - - +
128P VAL* 3.7 10.5 - - + -
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Residues in contact with VAL 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P GLU 3.3 4.3 - - - +
34P VAL* 4.5 5.4 - - + -
48P ALA 3.6 0.4 + - - +
49P VAL* 1.3 74.6 - - - +
51P LYS* 1.3 57.3 + - - +
52P ILE* 3.5 27.5 + - + +
74P ALA* 4.2 6.1 - - + -
76P LEU* 3.4 33.7 - - + -
126P GLU 2.7 18.2 - - - +
127P ILE* 3.0 13.9 + - + +
129P PHE* 3.6 17.7 - - + -
151P LEU* 3.3 39.5 - - + -
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Residues in contact with LYS 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ALA* 3.6 3.1 - - - -
33P GLU* 3.1 51.1 + - + +
35P GLU* 3.1 31.7 + - + +
49P VAL* 3.5 33.0 - - + +
50P VAL* 1.3 73.2 - - - +
52P ILE* 1.3 62.8 + - - +
53P PRO* 3.4 15.0 - - + +
125P GLN 3.5 8.3 - - - +
126P GLU* 3.2 23.9 + - - +
153P ALA* 4.5 0.7 - - - +
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Residues in contact with ILE 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P VAL* 3.5 15.7 + - + +
51P LYS* 1.3 75.8 - - - +
53P PRO* 1.3 61.7 - - - +
54P TYR* 5.0 0.3 - - - +
72P VAL* 4.3 12.8 - - + +
73P GLY 3.0 29.2 - - - +
74P ALA* 3.9 1.1 - - + -
124P TYR 4.9 2.0 - - - +
125P GLN* 3.1 30.1 + - - +
127P ILE* 3.6 27.1 - - + -
153P ALA* 3.2 22.2 - - + -
154P ASN 2.9 29.2 - - - +
155P ARG* 3.4 27.0 + - + +
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Residues in contact with PRO 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P LYS* 5.4 0.7 - - - +
31P PRO* 3.7 33.3 - - + +
32P ALA* 4.6 1.1 - - - +
51P LYS* 3.4 16.8 - - + +
52P ILE* 1.3 89.9 - - - +
54P TYR* 1.3 68.9 + - - +
125P GLN* 3.8 9.4 - - + +
155P ARG* 3.0 26.4 + - - +
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Residues in contact with TYR 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P LYS* 4.7 20.2 - - + -
52P ILE 5.0 0.4 - - - +
53P PRO* 1.3 81.5 - - - +
55P ASP* 1.3 87.2 + - - +
56P THR* 3.0 5.2 + - - +
57P LYS 3.3 9.0 - - - -
58P LEU* 2.8 47.4 - - + +
70P LEU* 3.4 29.8 - - + -
125P GLN* 2.6 26.1 + - - +
155P ARG* 4.7 15.3 - - + +
237P VAL* 4.4 21.9 + - + +
238P GLY* 6.4 0.2 - - - -
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Residues in contact with ASP 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P TYR* 1.3 82.4 - - - +
56P THR* 1.3 54.6 + - - +
57P LYS* 2.6 67.0 + - + +
58P LEU* 3.7 6.4 - - - +
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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