Contacts of the strand formed by residues 47 - 55 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU 3.9 3.5 - - - +
36C VAL* 4.1 0.3 - - - -
37C PRO* 3.6 15.2 - - + +
46C PHE* 1.3 93.4 - - - +
48C ALA* 1.3 70.9 + - - +
49C VAL* 3.4 30.0 - - + +
94C LEU 4.3 12.5 + - - -
95C LYS* 4.8 12.8 - - + +
98C VAL* 3.9 23.2 - - - +
128C VAL* 3.6 21.7 - - + +
129C PHE 3.6 3.6 - - - -
130C PRO* 5.1 0.7 - - - -
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 5.6 0.9 - - + -
35C GLU 3.3 8.1 - - - -
36C VAL* 3.8 16.6 - - + -
47C LYS* 1.3 79.1 - - - +
49C VAL* 1.3 61.7 + - - +
50C VAL* 4.6 1.2 - - - +
76C LEU* 4.8 10.1 - - + -
78C LEU* 5.5 2.9 - - + -
129C PHE* 3.0 53.6 + - + +
131C VAL* 3.9 13.7 - - + -
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU 3.5 1.9 - - - +
34C VAL* 3.4 3.1 - - - -
35C GLU* 2.8 40.8 + - + +
47C LYS* 3.4 32.8 - - + -
48C ALA* 1.3 70.9 - - - +
50C VAL* 1.3 61.5 + - - +
51C LYS* 3.4 35.4 + - + +
126C GLU* 3.4 32.5 - - + +
127C ILE 3.7 3.6 - - - +
128C VAL* 3.8 11.4 - - + -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU 3.2 3.6 - - - +
34C VAL* 4.5 6.3 - - + -
48C ALA 3.7 0.6 + - - +
49C VAL* 1.3 72.1 - - - +
51C LYS* 1.3 58.6 + - - +
52C ILE* 3.5 27.0 + - + +
74C ALA* 4.2 6.1 - - + -
76C LEU* 3.5 32.5 - - + -
126C GLU 2.7 18.6 - - - +
127C ILE* 3.0 14.0 + - + +
129C PHE* 3.7 17.9 - - + -
151C LEU* 3.3 40.2 - - + -
153C ALA* 4.5 0.2 - - + -
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA* 3.6 3.1 - - - -
33C GLU* 3.0 53.2 + - + +
35C GLU* 3.1 30.1 + - - +
49C VAL* 3.4 34.3 - - + +
50C VAL* 1.3 69.8 - - - +
52C ILE* 1.3 63.5 + - - +
53C PRO* 3.3 14.4 - - + +
125C GLN 3.5 7.2 - - - +
126C GLU* 3.2 24.7 + - - +
153C ALA* 4.5 0.7 - - - +
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Residues in contact with ILE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C VAL* 3.5 15.2 + - + +
51C LYS* 1.3 78.1 - - - +
53C PRO* 1.4 63.0 - - - +
54C TYR* 5.1 0.2 - - - +
72C VAL* 4.2 15.9 - - + +
73C GLY 3.0 29.2 - - - +
74C ALA* 4.0 0.9 - - + -
124C TYR 4.9 1.3 - - - +
125C GLN* 3.0 30.2 + - - +
127C ILE* 3.5 27.4 - - + -
153C ALA* 3.3 22.0 - - + -
154C ASN 2.9 29.2 - - - +
155C ARG* 3.5 22.1 + - - +
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Residues in contact with PRO 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LYS* 5.4 0.7 - - - +
31C PRO* 3.8 33.3 - - + +
32C ALA* 4.7 0.9 - - - +
51C LYS* 3.3 16.4 - - + +
52C ILE* 1.4 90.8 - - - +
54C TYR* 1.3 69.2 + - - +
125C GLN* 3.9 9.6 - - + +
155C ARG* 3.0 26.4 + - - +
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Residues in contact with TYR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LYS* 4.6 20.0 - - + -
52C ILE 5.1 0.7 - - - +
53C PRO* 1.3 80.7 - - - +
55C ASP* 1.3 78.0 + - - +
56C THR* 3.0 5.1 + - - +
57C LYS 3.3 18.4 - - - -
58C LEU* 2.8 46.7 - - + +
70C LEU* 3.4 27.8 - - + -
125C GLN* 2.6 25.3 + - - +
155C ARG* 4.7 15.3 - - + +
237C VAL* 4.4 22.4 + - + +
238C GLY* 6.4 0.2 - - - -
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Residues in contact with ASP 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TYR* 1.3 81.6 - - - +
56C THR* 1.3 53.9 + - - +
57C LYS* 2.6 67.7 + - + +
58C LEU* 3.7 6.1 - - - +
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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