Contacts of the strand formed by residues 75 - 83 (chain Q) 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 ALA 75 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74Q ASN* 1.3 82.5 - - + +
76Q GLY* 1.3 58.6 + - - +
77Q ASP* 3.4 2.8 + - - -
93Q VAL 4.0 1.1 - - - -
94Q GLU* 3.7 10.3 - - - -
117Q TRP* 3.3 20.0 - - + -
119Q ALA* 6.5 0.7 - - + -
122Q ASN* 5.5 0.9 + - - +
135Q GLU* 4.3 7.6 - - - +
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Residues in contact with GLY 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Q ASN 3.4 0.4 - - - -
75Q ALA* 1.3 71.9 - - - +
77Q ASP* 1.3 59.1 + - - -
78Q ARG* 3.1 20.4 + - - -
93Q VAL* 2.6 39.9 + - - +
100Q ARG* 4.2 0.2 - - - -
117Q TRP* 2.8 32.7 - - - -
135Q GLU* 4.8 0.4 - - - -
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Residues in contact with ASP 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Q SER 4.0 4.0 - - - +
73Q HIS* 2.4 68.4 + - + +
74Q ASN* 2.6 24.3 + - - +
75Q ALA 3.4 3.3 + - - -
76Q GLY* 1.3 74.6 + - - -
78Q ARG* 1.3 67.3 - - - +
79Q VAL* 3.8 3.5 + - + -
90Q TYR* 5.0 0.2 - - - -
92Q VAL* 3.4 9.2 + - - +
93Q VAL* 2.7 7.6 - - - +
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Residues in contact with ARG 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Q LYS* 4.3 10.9 - - - +
76Q GLY* 3.1 24.9 + - - -
77Q ASP* 1.3 73.3 - - - +
79Q VAL* 1.3 67.0 + - - +
90Q TYR* 4.0 20.6 - - + +
92Q VAL* 3.3 26.3 - - - +
100Q ARG* 2.5 36.9 - - - +
104Q ILE* 5.3 2.2 - - - -
117Q TRP* 2.9 73.7 - - + +
124Q PHE* 5.2 4.2 - - + -
135Q GLU* 2.8 14.7 + - - +
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Residues in contact with VAL 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Q ASP* 2.8 45.8 - - - +
59Q LYS* 3.7 19.7 - - + -
64Q VAL* 3.3 7.6 - - + +
69Q PHE* 3.4 25.8 - - + -
73Q HIS* 4.2 11.6 + - + -
77Q ASP* 3.8 4.2 + - + -
78Q ARG* 1.3 83.5 - - - +
80Q LEU* 1.3 59.5 + - - +
90Q TYR* 2.9 31.1 - - - +
91Q ILE 4.2 0.2 + - - -
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Residues in contact with LEU 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE* 3.3 59.9 - - + +
57Q LYS 2.7 24.8 - - - +
58Q ASP* 3.5 8.8 - - - +
59Q LYS* 5.3 3.9 - - + +
64Q VAL* 3.0 6.4 - - - +
79Q VAL* 1.3 74.6 - - - +
81Q VAL* 1.3 71.4 + - - +
82Q GLN 3.7 4.5 - - - +
87Q ASP 5.7 0.2 - - - +
88Q PRO* 4.5 17.7 - - + -
89Q THR 3.1 18.2 - - - +
90Q TYR* 4.6 9.0 - - + +
114Q VAL* 5.5 8.1 - - + -
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Residues in contact with VAL 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE* 4.3 0.5 - - - -
56Q ALA* 3.2 23.3 - - + +
57Q LYS* 3.3 17.5 + - - +
64Q VAL* 2.9 38.5 - - + +
80Q LEU* 1.3 81.8 - - - +
82Q GLN* 1.3 73.8 + - + +
89Q THR* 2.8 24.0 + - + +
90Q TYR 3.1 24.2 - - - +
91Q ILE* 4.1 1.3 - - + -
160Q ILE 5.2 7.4 - - - +
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Residues in contact with GLN 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE* 4.4 12.1 - - + -
51Q GLY 2.5 31.8 + - - +
52Q GLY* 4.1 2.2 - - - -
53Q GLY 3.4 11.4 + - - -
54Q THR* 3.8 9.0 + - - -
55Q THR* 3.6 11.2 + - - -
56Q ALA 3.4 11.6 - - - +
57Q LYS* 2.8 43.8 - - + +
80Q LEU* 3.8 10.4 - - - +
81Q VAL* 1.3 89.5 - - + +
83Q GLY* 1.3 53.6 + - - +
87Q ASP 2.4 23.0 - - - +
88Q PRO* 3.5 5.4 - - - +
89Q THR* 2.1 26.0 + - - -
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Residues in contact with GLY 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Q GLY* 3.1 30.5 - - - +
82Q GLN* 1.3 80.0 - - - +
84Q LEU* 1.3 59.1 + - - -
85Q LYS 3.6 2.6 + - - -
86Q GLY* 4.1 2.2 - - - -
87Q ASP 2.7 23.1 - - - -
89Q THR* 3.3 15.1 - - - +
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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