Contacts of the strand formed by residues 96 - 103 (chain A) in PDB entry 6YB9
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 ILE 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ILE* 2.8 23.5 + - + +
95A PRO* 1.3 83.2 - - + +
97A GLU* 1.3 73.2 + - - +
98A TRP* 3.4 42.8 - - + +
128A LEU* 4.1 15.3 - - + -
129A PHE 3.3 4.9 - - - +
130A PHE* 3.9 20.6 - - + +
131A LYS* 4.1 2.0 - - - +
140A TRP* 4.0 15.9 - - + -
145A LEU* 3.9 35.0 - - + -
150A PHE* 5.0 1.1 - - + -
193A GLU* 3.9 15.2 - - - +
194A PHE 4.9 0.2 + - - -
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Residues in contact with GLU 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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96A ILE* 1.3 71.3 - - - +
98A TRP* 1.3 59.8 + - - +
99A VAL* 3.9 1.1 - - + -
127A GLU 3.7 1.4 - - - +
128A LEU* 3.5 5.4 - - - -
129A PHE* 2.7 52.5 + - + +
131A LYS* 3.2 29.0 + - + +
137A ASP* 3.2 19.1 - - - +
191A LYS* 3.7 19.5 + - + -
192A ILE 4.0 4.5 - - - -
193A GLU* 3.8 16.6 - - - +
502A OK8 3.2 18.5 + - - +
508A MG 2.1 30.8 - - - -
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Residues in contact with TRP 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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96A ILE* 3.4 31.4 + - + +
97A GLU* 1.3 69.4 - - - +
99A VAL* 1.3 61.2 + - - +
126A VAL* 4.1 12.8 - - + -
127A GLU 3.6 4.0 - - - -
128A LEU* 3.7 34.3 - - + -
142A GLU* 5.6 0.2 - - - -
145A LEU* 3.8 20.2 - - + -
162A VAL* 3.9 13.2 - - + -
165A MET* 3.3 49.5 - - + +
166A SER* 3.8 22.2 - - - -
169A THR* 3.5 30.0 - - + +
190A MET* 3.9 0.5 - - - +
191A LYS* 3.2 3.5 - - - -
192A ILE* 3.0 43.1 + - + +
194A PHE* 3.5 17.9 - + - -
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Residues in contact with VAL 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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97A GLU* 4.6 1.6 - - + +
98A TRP* 1.3 76.3 - - - +
100A CYS* 1.3 63.7 - - - +
101A ARG* 3.8 38.8 - - + +
125A LYS 3.7 0.8 - - - +
126A VAL* 3.2 8.3 - - - +
127A GLU* 2.8 38.2 + - + +
129A PHE* 3.7 28.0 - - + -
169A THR* 4.2 2.5 - - - -
190A MET 3.2 11.2 - - - +
191A LYS* 4.2 10.8 - - + -
502A OK8 3.9 31.4 - - + +
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Residues in contact with CYS 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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98A TRP 4.3 0.2 - - - -
99A VAL* 1.3 74.7 - - - +
101A ARG* 1.3 62.4 + - - +
102A ARG 4.4 0.2 - - - -
124A PRO* 3.4 31.2 - - - -
125A LYS 3.1 7.2 - - - -
126A VAL* 4.2 7.0 - - - -
169A THR* 4.0 12.3 - - + +
170A GLN* 4.0 15.9 - - - -
173A PHE* 3.6 36.0 - - + -
189A ASP* 3.1 6.8 - - - +
190A MET* 3.0 32.2 + - + -
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Residues in contact with ARG 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 VAL* 3.8 16.5 - - + +
100A CYS* 1.3 78.5 - - - +
102A ARG* 1.3 57.7 + - - +
103A ILE 4.2 8.7 - - - +
105A THR 3.6 14.1 + - - +
107A SER* 3.1 9.7 + - - -
108A PHE* 3.8 28.5 - - - +
111A ARG* 3.7 2.6 - - - +
121A PHE* 3.6 25.3 - - + +
124A PRO* 3.2 10.8 - - - +
125A LYS* 2.8 36.2 + - + +
127A GLU* 2.9 31.8 + - - -
129A PHE* 4.1 3.4 - - - -
173A PHE* 4.5 0.7 - - - -
188A VAL 3.8 4.0 - - - -
189A ASP* 3.7 13.9 + - + +
502A OK8 3.1 49.5 + - - -
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Residues in contact with ARG 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 ARG* 1.3 72.4 - - - +
103A ILE* 1.3 71.4 + - + +
120A LYS* 3.4 13.5 - - + +
121A PHE* 2.9 51.6 + - - +
122A TYR* 3.7 11.9 - - - +
123A PRO* 4.6 0.6 - - - +
124A PRO* 3.5 30.7 - - - +
173A PHE* 3.7 11.8 - - + -
174A GLU* 4.5 5.5 - - - +
177A GLU* 2.7 45.5 + - - +
186A THR* 6.0 1.3 - - + -
187A LEU 4.0 5.4 - - - +
188A VAL 2.9 12.5 + - - +
314B ALA 4.9 1.2 + - - -
317B GLU 4.8 1.4 + - - -
318B GLY* 3.5 40.2 + - - +
701B EDO 4.2 1.4 - - - -
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Residues in contact with ILE 103 (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 ARG* 4.2 8.5 - - - +
102A ARG* 1.3 87.2 - - + +
104A ALA* 1.3 68.7 + - - +
105A THR* 3.3 3.8 + - - +
118A GLY* 3.6 27.6 - - - +
119A TYR 3.4 2.9 - - - -
120A LYS* 3.7 30.5 - - + +
121A PHE* 4.0 3.4 - - - -
186A THR* 3.7 29.2 - - + -
188A VAL* 3.3 33.7 + - + +
189A ASP* 4.6 2.1 - - - +
217A TRP* 4.5 24.5 - - + -
220A GLY* 6.4 0.2 - - - -
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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