Contacts of the strand formed by residues 92 - 99 (chain H) in PDB entry 4G5Z
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 92 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG* 3.9 11.9 - - + -
39H GLN 3.3 29.4 - - - +
40H ALA* 3.7 4.7 - - + +
41H PRO* 4.7 2.5 - - - -
89H GLU 5.5 0.2 - - - +
90H ASP 3.1 11.0 + - - +
91H THR* 1.3 76.7 - - - +
93H VAL* 1.3 59.6 + - - +
94H TYR* 3.2 18.8 - - + -
113H LEU* 3.9 8.7 - - - -
114H VAL 3.0 28.5 + - - -
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ARG* 3.3 4.3 - - - -
39H GLN* 2.9 38.3 + - + +
92H ALA* 1.3 71.2 - - - +
94H TYR* 1.3 61.1 + - - +
95H TYR* 3.6 35.8 + - + +
110H GLN 4.6 1.8 - - - +
111H GLY* 3.9 19.7 - - - -
112H THR 3.6 8.3 - - - +
113H LEU* 4.1 21.1 - - + +
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Residues in contact with TYR 94 (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* 3.8 7.4 - - - +
20H LEU* 3.6 19.5 - - + -
36H TRP* 4.1 8.5 - + + -
37H VAL 3.8 2.7 - - - -
38H ARG* 2.9 41.7 + - + -
48H VAL* 4.5 6.3 - - + -
68H PHE* 3.9 14.1 - + - -
81H LEU* 3.9 18.4 - - + -
83H MET* 3.9 16.6 - - - -
90H ASP* 2.7 35.2 + - - +
92H ALA* 3.2 20.6 - - + -
93H VAL* 1.3 71.7 - - - +
95H TYR* 1.4 60.7 + - - +
111H GLY* 3.3 2.1 - - - -
112H THR* 2.8 35.3 + - + +
114H VAL* 3.7 24.0 - - + -
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Residues in contact with TYR 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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6H GLU* 3.3 4.9 - - - +
36H TRP* 3.3 11.1 - - - -
37H VAL* 2.7 46.4 + - - +
38H ARG* 4.9 0.4 - - - -
39H GLN* 4.0 15.9 + - + -
45H LEU* 4.4 6.5 - - + -
93H VAL* 3.6 28.3 - - + +
94H TYR* 1.4 73.5 - - - +
96H CYS* 1.3 61.4 + - - +
97H ALA 4.0 0.2 + - - -
108H TRP* 3.8 29.8 - + + -
109H GLY 3.5 20.6 - - - -
110H GLN 3.5 20.8 + - - -
111H GLY* 3.7 8.1 - - - -
38L GLN* 3.3 29.1 + - - -
41L ASP* 4.5 8.1 + - - -
42L GLN 3.3 8.5 + - - -
43L SER* 4.0 12.3 - - - -
44L PRO* 4.0 6.7 - - + -
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Residues in contact with CYS 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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4H LEU* 3.6 6.9 - - + +
6H GLU* 2.8 19.7 + - + +
22H CYS* 2.0 54.3 - - + -
34H MET* 3.5 25.1 - - - -
35H ASN 3.5 4.3 - - - -
36H TRP* 4.1 5.6 - - + -
79H LEU* 3.8 5.8 - - - -
95H TYR* 1.3 73.2 - - - +
97H ALA* 1.3 59.4 + - - +
108H TRP* 3.4 3.1 - - - +
109H GLY 3.0 26.5 + - - -
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Residues in contact with ALA 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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4H LEU* 4.1 0.4 - - - -
34H MET* 3.8 5.5 - - - -
35H ASN* 2.8 49.8 + - + +
37H VAL* 4.5 7.4 - - + -
95H TYR 5.0 0.2 - - - +
96H CYS* 1.3 76.2 - - - +
98H ARG* 1.3 62.2 + - - +
105H PHE* 3.9 25.8 - - + -
107H TYR 3.3 8.7 - - - +
108H TRP* 4.0 19.1 - - + -
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Residues in contact with ARG 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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2H VAL* 3.6 16.7 - - - +
4H LEU* 3.7 10.4 - - + +
27H PHE* 3.4 45.9 - - - +
32H TYR* 3.4 54.4 + - + -
34H MET* 3.8 15.5 - - - -
35H ASN* 4.5 0.7 - - - -
97H ALA* 1.3 70.5 - - - +
99H ASP* 1.3 60.4 + - - +
100H LEU* 5.7 0.2 - - - +
105H PHE* 3.1 8.4 - - - -
106H ASP* 2.8 63.4 + - - +
107H TYR* 2.9 37.2 + - + +
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Residues in contact with ASP 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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32H TYR* 3.3 22.7 - - - +
33H GLY* 3.1 33.3 + - - +
35H ASN* 3.2 24.1 + - - +
50H ILE* 3.4 16.7 - - - +
52H TRP* 5.4 0.5 + - - -
97H ALA 3.7 0.4 + - - -
98H ARG* 1.3 71.9 - - - +
100H LEU* 1.3 58.7 + - - +
101H ARG 3.6 2.6 + - - -
102H THR* 2.9 43.4 + - - +
103H GLY 3.9 2.1 + - - +
104H PRO 3.9 1.6 - - - -
105H PHE* 3.5 14.8 - - - -
106H ASP* 4.8 0.2 - - - -
96L PHE* 5.3 0.3 - - - -
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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