Contacts of the strand formed by residues 92 - 97 (chain A) in PDB entry 1JBS
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 TYR 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP* 3.5 15.2 + - + +
50A TRP* 3.7 20.0 - + + +
79A PRO* 3.6 20.2 - - + -
80A LYS 3.6 9.0 - - - -
81A HIS* 3.3 35.4 - + + -
85A GLY* 2.4 33.9 + - - -
90A ASP* 4.0 5.8 - - + -
91A HIS* 1.3 75.5 - - - +
93A LEU* 1.3 74.9 + - - +
94A LEU* 3.5 25.4 - - + +
124A THR* 3.5 3.6 - - - -
125A TYR* 2.7 58.1 + + + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TRP* 3.2 10.7 - - - -
51A PHE* 2.7 59.6 + - + +
53A ASN* 3.9 15.9 - - + +
70A PHE* 3.8 22.9 - - + -
74A ASP 4.7 1.8 - - - +
75A CYS* 3.7 23.1 - - - +
77A ARG 6.0 1.6 - - - +
79A PRO* 5.0 2.8 - - + +
92A TYR* 1.3 80.0 - - - +
94A LEU* 1.3 54.5 + - - +
122A ILE* 3.9 11.7 - - + -
123A TYR 3.6 2.5 - - - +
124A THR* 4.1 10.5 - - + -
131A CYS* 3.7 28.7 - - - -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO 4.9 0.7 - - - +
38A LEU* 4.3 20.4 - - + -
39A SER 3.7 26.2 - - - +
40A ASP* 4.5 0.9 - - - -
48A PRO* 4.6 4.7 - - + -
49A HIS* 3.5 22.9 - - - +
50A TRP 3.8 0.7 - - - +
51A PHE* 4.2 2.5 - - - -
92A TYR* 3.5 31.2 - - + +
93A LEU* 1.3 74.1 - - - +
95A GLU* 1.3 59.6 + - - +
121A VAL 3.6 0.9 - - - +
122A ILE* 3.4 6.6 - - - +
123A TYR* 2.8 70.7 + - + +
125A TYR* 4.3 12.6 - - + -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 3.4 11.0 + - + -
48A PRO* 3.3 7.7 - - - +
49A HIS* 3.0 57.4 + - - +
50A TRP 4.6 0.5 - - - +
51A PHE* 3.7 22.6 - - + +
94A LEU* 1.3 74.6 - - - +
96A PHE* 1.3 61.8 + - - +
120A ARG* 2.9 32.6 + - + +
121A VAL 3.6 4.7 - - - -
122A ILE* 3.5 20.2 - - + -
144A LEU* 3.8 14.4 - - - +
17C A 5.8 3.3 - - - +
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASN* 4.0 25.4 - - + -
36A ALA* 3.4 27.6 - - + -
47A TYR* 3.9 4.5 - - + -
48A PRO* 3.5 33.0 - - + -
95A GLU* 1.3 76.2 - - - +
97A PRO* 1.3 91.5 - - + +
104A ASP* 5.4 1.1 - - + -
105A TYR* 3.7 43.3 - + + -
107A PHE* 3.8 18.6 - + + -
120A ARG* 3.2 6.4 - - - +
121A VAL* 2.8 32.8 + - + +
123A TYR* 3.7 20.9 - + + +
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Residues in contact with PRO 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASN* 4.6 4.5 - - - +
47A TYR* 3.6 23.3 - - + -
96A PHE* 1.3 116.7 - - + +
98A THR* 1.3 60.3 + - - +
99A PHE* 3.9 8.2 - - + -
105A TYR* 3.7 34.5 + - + +
116A PRO* 3.5 38.6 - - + +
119A ALA 3.6 8.5 - - - +
120A ARG* 3.9 3.1 - - - -
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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