Contacts of the strand formed by residues 91 - 96 (chain H) in PDB entry 1AJ7
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 91 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H LYS* 3.9 24.9 - - + -
39H GLN 3.3 14.4 - - - +
40H ARG* 3.3 14.8 - - + +
41H PRO* 6.2 0.9 - - - -
89H ASP 3.1 3.4 + - - -
90H THR* 1.3 78.3 - - - +
92H VAL* 1.3 64.8 + - - +
93H TYR* 3.7 10.1 - - + -
107H THR 3.6 1.0 - - - +
108H THR* 3.6 4.0 - - - +
109H LEU 2.8 30.9 + - - +
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Residues in contact with VAL 92 (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 3.9 0.3 - - - +
38H LYS* 3.6 2.3 - - - -
39H GLN* 2.9 41.4 + - + +
91H ALA* 1.3 78.5 - - - +
93H TYR* 1.3 62.9 + - - +
94H TYR* 3.7 33.0 + - + +
105H GLN 5.2 0.7 - - - +
106H GLY* 4.0 4.5 - - - -
107H THR 3.2 21.8 - - - +
108H THR* 3.7 22.9 - - + +
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Residues in contact with TYR 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLN* 2.8 23.8 + - - -
20H LEU* 3.6 28.3 - - + -
36H TRP* 4.5 7.6 - - + -
37H VAL 3.2 5.8 - - - +
38H LYS* 3.8 25.1 + - + +
48H ILE* 3.7 27.6 - - + -
63H PHE* 5.6 0.8 - + - -
80H LEU* 3.9 7.4 - - + -
82H LEU* 3.7 24.3 - - + +
89H ASP* 2.7 41.1 + - - +
91H ALA* 3.7 23.6 - - + -
92H VAL* 1.3 74.7 - - - +
94H TYR* 1.3 56.7 + - - +
106H GLY* 3.2 1.2 - - - -
107H THR 2.8 25.7 + - - +
109H LEU* 3.8 13.9 - - + -
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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 GLN* 3.4 5.2 - - - -
36H TRP* 3.3 7.5 - - - -
37H VAL* 2.7 45.0 + - + +
39H GLN* 3.4 28.4 + - + -
45H LEU* 4.8 4.0 - - + -
92H VAL* 3.7 24.9 - - + +
93H TYR* 1.3 76.3 - - - +
95H CYS* 1.3 59.6 + - - +
103H TRP* 3.9 20.9 - + + -
104H GLY 3.4 19.7 - - - -
105H GLN 3.8 8.9 + - - -
106H GLY* 3.6 17.0 - - - -
38L GLN* 3.0 23.6 + - - -
42L GLY* 3.1 26.6 + - - -
44L ILE* 4.2 17.9 - - + -
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Residues in contact with CYS 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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4H LEU* 3.7 2.6 - - - +
6H GLN* 3.1 28.2 + - - -
22H CYS* 2.0 54.1 - - + -
34H MET* 4.9 3.8 - - + -
35H HIS 3.1 8.5 - - - +
36H TRP* 4.1 15.5 - - + -
94H TYR* 1.3 74.7 - - - +
96H ALA* 1.3 63.4 + - - +
103H TRP* 3.6 3.1 - - - -
104H GLY* 2.9 33.1 + - - -
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Residues in contact with ALA 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* 3.9 4.7 - - - -
34H MET* 3.4 7.5 - - - +
35H HIS* 2.8 36.1 + - + +
37H VAL* 5.4 0.7 - - + -
95H CYS* 1.3 75.5 - - - +
97H SER* 1.3 65.6 + - - +
100H GLY* 4.7 1.6 - - - -
102H TYR 3.3 12.1 - - - +
103H TRP* 3.8 21.8 - - + +
217H NPE 3.5 24.7 - - - +
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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