Contacts of the strand formed by residues 96 - 102 (chain A) in PDB entry 5J1T
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 LEU 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ALA 3.6 28.0 - - - +
83A VAL* 4.2 10.5 - - + -
86A PHE* 3.4 39.2 - - + -
94A LYS 3.4 3.7 + - - -
95A PRO* 1.3 69.8 - - - +
97A THR* 1.3 62.1 + - - +
98A LEU* 4.0 17.3 - - + -
201A ALA 3.2 5.9 + - - -
202A MET* 3.4 18.0 - - + +
203A PHE 2.9 26.5 + - - +
264A ASP* 3.7 7.0 - - + +
265A TYR* 3.9 33.9 - - + -
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Residues in contact with THR 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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94A LYS* 3.3 6.6 + - - -
95A PRO* 3.2 13.0 + - - +
96A LEU* 1.3 77.2 + - - +
98A LEU* 1.3 60.5 + - - +
187A LEU* 3.9 18.3 + - + +
203A PHE* 3.3 9.5 - - + +
205A PHE* 3.7 35.7 - - + -
262A LEU 3.3 24.3 + - - +
263A ILE* 3.8 9.7 - - + +
264A ASP* 2.9 37.6 + - - +
265A TYR 3.3 7.4 + - - -
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Residues in contact with LEU 98 (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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79A ILE* 3.9 22.7 - - + -
82A ALA* 4.1 8.3 - - + -
83A VAL* 4.2 18.2 - - + -
96A LEU* 4.0 20.4 - - + +
97A THR* 1.3 77.4 - - - +
99A SER* 1.3 60.3 + - - +
100A LEU* 3.7 13.9 - - + -
115A ILE* 4.4 5.8 - - + -
202A MET* 4.8 1.6 - - - -
203A PHE 2.9 11.3 + - - +
204A ILE* 3.6 19.5 - - + -
205A PHE* 2.8 31.3 + - - +
263A ILE* 4.6 1.3 - - - -
265A TYR* 3.5 38.1 - - + +
267A VAL* 4.7 4.0 - - + -
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Residues in contact with SER 99 (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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98A LEU* 1.3 73.8 - - - +
100A LEU* 1.3 60.6 + - - +
101A HIS* 3.6 10.0 + - - +
172A MET* 5.9 2.8 - - - -
205A PHE* 3.6 14.9 + - - +
207A SER* 5.0 3.3 + - - -
263A ILE* 3.8 31.7 - - - +
265A TYR 2.9 9.3 + - - -
266A PHE* 3.5 17.3 - - - -
267A VAL 2.8 30.8 + - - -
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Residues in contact with LEU 100 (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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79A ILE* 4.3 8.1 - - + -
98A LEU* 3.7 25.4 - - + -
99A SER* 1.3 73.8 + - - +
101A HIS* 1.3 60.6 + - - +
108A LYS* 3.6 21.1 - - + +
111A VAL* 4.1 15.0 - - + -
112A SER* 4.1 5.6 - - - +
115A ILE* 5.2 1.3 - - + -
204A ILE* 4.1 11.7 - - + -
205A PHE 2.7 14.6 + - - +
206A LEU* 3.4 22.3 - - + -
207A SER* 3.0 24.6 + - - +
267A VAL* 3.5 19.1 - - + -
269A PHE* 3.8 26.5 - - + -
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Residues in contact with HIS 101 (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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99A SER* 3.6 14.9 + - - +
100A LEU* 1.3 77.9 - - - +
102A GLY* 1.3 58.4 + - - +
108A LYS* 4.0 3.7 - - - +
207A SER* 3.1 17.3 - - - +
209A ALA* 3.2 25.6 - - + +
214A ILE* 3.5 15.0 - - + +
236A ILE* 5.5 1.1 - - + -
240A LEU* 3.6 26.8 - - + +
244A VAL* 4.7 7.3 - - + +
245A PHE* 4.7 2.2 - + - -
266A PHE* 3.9 32.8 - + + +
267A VAL 3.0 19.6 + - - -
268A PRO* 3.3 13.8 - - + +
269A PHE* 2.9 22.5 + - - -
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Residues in contact with GLY 102 (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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101A HIS* 1.3 74.9 - - - +
103A TRP* 1.3 68.4 + - - -
108A LYS* 3.1 15.3 + - - +
207A SER 3.1 6.7 + - - -
208A ASN* 3.1 17.0 + - - +
209A ALA 4.3 0.4 + - - -
211A ALA* 3.7 16.8 - - - +
214A ILE* 4.1 7.6 - - - -
269A PHE* 3.6 12.6 - - - -
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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