Contacts of the strand formed by residues 94 - 100 (chain H) in PDB entry 1V7M
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 GLY 94 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38H ARG* 5.3 0.9 - - - -
39H GLN 3.1 13.9 - - - -
40H SER* 4.7 2.0 - - - -
92H ASP 3.6 1.4 + - - -
93H THR* 1.3 77.2 - - - +
95H ILE* 1.3 66.0 + - - -
96H TYR* 3.1 12.5 - - - -
111H LEU* 3.8 12.1 - - - +
112H VAL 3.0 27.0 + - - -
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Residues in contact with ILE 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H VAL 4.0 0.5 - - - +
38H ARG* 3.2 4.2 - - - -
39H GLN* 2.7 46.3 + - + +
94H GLY* 1.3 71.0 - - - -
96H TYR* 1.3 61.7 + - - +
97H TYR* 3.8 29.0 - - + +
108H GLN 4.7 1.8 - - - +
109H GLY* 3.7 29.6 - - - -
110H THR 3.5 7.0 - - - +
111H LEU* 4.2 17.3 - - + +
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Residues in contact with TYR 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLU* 4.1 2.8 - - - +
20H LEU* 3.5 30.5 - - + -
36H TRP* 4.6 7.6 - + + -
37H VAL 3.8 3.6 - - - -
38H ARG* 3.1 42.2 + - + -
48H VAL* 4.6 7.9 - - + -
70H PHE* 4.1 10.1 - + - -
83H LEU* 4.3 9.9 - - + -
85H MET* 3.9 16.8 - - - -
92H ASP* 2.5 42.6 + - - +
94H GLY 3.1 25.8 - - - -
95H ILE* 1.3 74.7 - - - +
97H TYR* 1.4 60.4 + - - +
109H GLY* 3.0 2.5 - - - -
110H THR* 2.6 44.0 + - - +
112H VAL* 3.7 21.1 - - + -
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Residues in contact with TYR 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLU* 3.3 4.0 - - - -
35H ASP 3.8 0.2 - - - +
36H TRP* 3.6 9.7 - - - -
37H VAL* 3.1 46.6 + - + +
39H GLN* 3.0 39.1 + - + -
45H LEU* 4.8 2.2 - - + -
95H ILE* 3.8 29.0 - - + +
96H TYR* 1.4 72.5 - - - +
98H CYS* 1.3 61.9 + - - +
99H SER* 4.9 0.3 - - - -
106H TRP* 3.9 30.3 - + + -
107H GLY 3.8 9.6 - - - -
108H GLN 3.9 3.8 - - - -
109H GLY* 3.5 18.8 - - - -
37L GLN* 3.7 8.8 + - - -
41L THR 4.3 2.5 + - - -
42L SER* 3.6 21.5 - - - -
43L PRO* 3.9 14.0 - - + +
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Residues in contact with CYS 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.7 17.6 - - - +
6H GLU* 3.2 19.6 + - - +
22H CYS* 2.0 54.1 - - + -
34H MET* 4.5 2.7 - - + -
35H ASP 3.5 7.4 - - - +
36H TRP* 3.8 15.2 - - + -
81H VAL* 4.3 7.2 - - + -
97H TYR* 1.3 75.0 - - - +
99H SER* 1.3 60.6 + - - +
106H TRP* 3.5 2.1 - - - -
107H GLY 2.9 26.2 + - - -
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Residues in contact with SER 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 4.0 0.2 - - - -
34H MET* 3.3 9.4 - - - +
35H ASP* 3.0 38.9 + - - +
37H VAL* 5.0 1.8 - - - -
97H TYR 4.9 1.8 - - - -
98H CYS* 1.3 77.4 - - - +
100H GLY* 1.3 58.2 + - - +
103H PHE* 3.0 41.4 - - - -
105H TYR 2.9 15.6 + - - -
106H TRP* 3.7 18.1 - - - -
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Residues in contact with GLY 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.7 9.2 - - - +
27H PHE* 5.3 0.9 - - - -
32H ALA* 5.1 0.9 - - - -
33H TRP 3.7 4.9 - - - -
34H MET* 3.7 15.3 - - - -
99H SER* 1.3 74.6 + - - +
101H TRP* 1.3 70.2 + - - +
102H SER 3.5 2.0 - - - -
103H PHE 4.2 0.7 - - - -
104H LEU 3.3 1.9 + - - -
105H TYR* 2.8 39.6 + - - -
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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