Contacts of the strand formed by residues 92 - 99 (chain H) in PDB entry 3GIZ
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* 3.8 13.0 - - + +
39H GLN 3.5 30.1 - - - +
40H ALA* 3.9 4.5 - - + +
41H PRO* 4.6 3.6 - - - -
90H ASP 3.2 4.1 + - - +
91H THR* 1.3 78.7 - - - +
93H LEU* 1.3 58.5 + - - +
94H TYR* 3.3 20.4 - - + -
117H THR* 3.6 3.0 - - - -
118H VAL 2.8 34.3 + - - +
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Residues in contact with LEU 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ARG* 3.2 4.2 - - - -
39H GLN* 2.8 44.8 + - + +
41H PRO* 5.3 1.0 - - - +
92H ALA* 1.3 70.5 - - - +
94H TYR* 1.3 60.2 + - - +
95H TYR* 3.2 39.8 + - + +
114H GLN 3.8 8.7 - - - +
115H GLY* 3.3 35.7 - - - +
116H THR 3.4 11.4 - - - +
117H THR* 3.9 17.2 - - + +
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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
----------------------------------------------------------
6H GLU* 3.4 7.8 - - - +
20H LEU* 3.7 29.6 - - + -
36H TRP* 4.2 7.1 - + + -
37H VAL 3.7 2.5 - - - -
38H ARG* 3.2 39.4 + - + -
48H VAL* 4.2 11.2 - - + -
68H PHE* 4.2 8.3 - + - -
81H LEU* 4.4 6.7 - - + -
83H MET* 3.9 19.0 - - - -
90H ASP* 2.5 36.4 + - - +
92H ALA* 3.3 19.3 - - + -
93H LEU* 1.3 74.1 - - - +
95H TYR* 1.3 61.8 + - - +
115H GLY* 3.2 4.0 - - - -
116H THR* 2.8 34.9 + - + +
118H VAL* 3.6 23.5 - - + +
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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
----------------------------------------------------------
6H GLU* 3.5 2.5 - - - -
36H TRP* 3.2 11.5 - - - -
37H VAL* 2.7 47.2 + - + +
39H GLN* 3.9 19.9 + - + -
45H LEU* 4.4 7.4 - - + -
93H LEU* 3.2 30.4 - - + +
94H TYR* 1.3 75.6 - - - +
96H CYS* 1.3 60.1 + - - +
112H TRP* 3.7 33.7 - + + -
113H GLY 3.5 27.8 - - - -
114H GLN 3.5 14.3 + - - -
115H GLY* 4.0 7.6 - - - -
38L GLN* 3.6 15.1 + - - -
41L GLY 5.6 0.9 + - - -
42L GLN 3.8 4.0 + - - -
43L ALA* 3.6 22.0 + - + -
44L PRO* 4.1 7.0 - - + -
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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
----------------------------------------------------------
4H LEU* 3.7 14.3 - - - +
5H VAL 4.8 0.4 - - - -
6H GLU* 3.0 22.9 + - - -
22H CYS* 2.0 54.5 - - + -
34H MET* 4.4 0.9 - - + -
35H HIS 3.2 10.3 - - - +
36H TRP* 3.8 7.9 - - + -
79H LEU* 3.8 9.9 - - + -
95H TYR* 1.3 75.9 - - - +
97H ALA* 1.3 63.2 + - - +
112H TRP* 3.5 1.0 - - - -
113H GLY 3.1 25.8 + - - -
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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
----------------------------------------------------------
4H LEU* 3.9 0.9 - - - -
34H MET* 3.7 7.1 - - - -
35H HIS* 3.0 41.1 + - + -
37H VAL* 5.2 1.6 - - + -
96H CYS* 1.3 77.1 - - - +
98H LYS* 1.3 61.2 + - - +
109H MET* 4.0 18.2 - - + -
111H VAL 3.2 12.1 - - - +
112H TRP* 3.7 32.8 - - + -
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Residues in contact with LYS 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* 3.9 3.4 - - + +
27H PHE* 3.6 33.2 - - + -
32H TYR* 3.8 38.2 - - + -
34H MET* 3.7 15.9 - - - -
35H HIS* 4.5 0.7 - - - -
97H ALA* 1.3 72.7 - - - +
99H ASP* 1.3 75.4 + - - +
100H ILE* 3.9 6.7 - - - +
109H MET* 3.3 4.9 - - - -
110H ASP* 2.9 64.8 + - - +
111H VAL* 2.9 30.3 + - + +
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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 25.3 - - - +
33H ALA* 3.1 25.3 + - + +
35H HIS* 2.9 23.1 + - + -
97H ALA 3.9 1.4 + - - -
98H LYS* 1.3 82.1 + - - +
100H ILE* 1.3 57.3 + - - +
101H GLN* 3.0 34.1 + - + +
107H TYR* 3.5 3.5 - - - -
108H GLY 3.1 24.7 + - - +
91L ARG* 2.7 34.6 + - - -
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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
------------------------------------------------------------
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