Contacts of the strand formed by residues 96 - 103 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B ILE* 2.8 24.3 + - + +
95B PRO* 1.3 83.4 - - + +
97B GLU* 1.3 71.7 + - - +
98B TRP* 3.3 44.8 + - + +
128B LEU* 4.1 13.9 - - + -
129B PHE 3.3 4.5 - - - +
130B PHE* 3.9 19.3 - - + +
131B LYS* 4.1 2.3 - - - +
140B TRP* 3.9 19.5 - - + -
145B LEU* 3.8 34.5 - - + -
150B PHE* 4.8 0.9 - - + -
193B GLU* 3.9 14.9 - - - +
194B PHE 4.9 0.3 + - - -
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 1.3 71.2 - - - +
98B TRP* 1.3 60.4 - - - +
99B VAL* 3.9 1.3 - - + -
127B GLU 3.7 0.9 - - - +
128B LEU* 3.5 4.0 - - - -
129B PHE* 2.6 51.8 + - + +
131B LYS* 3.2 31.5 + - + +
137B ASP* 3.2 18.9 - - - +
191B LYS* 3.8 22.1 + - + -
192B ILE 3.9 4.0 - - - -
193B GLU* 3.8 16.3 - - - +
703B OK8 3.2 14.8 + - - +
706B MG 2.1 30.4 - - - -
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Residues in contact with TRP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 3.3 30.1 + - + +
97B GLU* 1.3 68.8 - - - +
99B VAL* 1.3 61.6 + - - +
126B VAL* 4.1 12.3 - - + -
127B GLU 3.5 4.0 - - - -
128B LEU* 3.6 35.2 - - + -
145B LEU* 3.8 22.0 - - + -
162B VAL* 3.9 13.0 - - + -
165B MET* 2.9 48.4 - - + +
166B SER* 3.8 22.0 - - - -
169B THR* 3.4 30.5 - - + +
190B MET* 3.9 0.7 - - - +
191B LYS* 3.3 2.1 - - - -
192B ILE* 3.0 44.7 + - + +
193B GLU* 4.6 1.3 - - - -
194B PHE* 3.5 17.5 - + - -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 4.5 0.9 - - + +
98B TRP* 1.3 77.6 - - - +
100B CYS* 1.3 63.3 + - - +
101B ARG* 3.7 29.2 - - + +
125B LYS 3.6 0.6 - - - +
126B VAL* 3.2 7.3 - - - +
127B GLU* 2.8 38.4 + - + +
129B PHE* 3.7 30.5 - - + -
169B THR* 4.3 2.0 - - - -
190B MET 3.2 9.9 - - - +
191B LYS* 4.2 11.0 - - + -
703B OK8 3.6 40.8 - - + +
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Residues in contact with CYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B TRP 4.3 0.2 + - - -
99B VAL* 1.3 76.0 - - - +
101B ARG* 1.3 61.0 + - - +
124B PRO* 3.4 33.0 - - - -
125B LYS 3.1 8.1 - - - -
126B VAL* 4.2 7.4 - - - -
169B THR* 4.0 12.3 - - + +
170B GLN* 4.1 15.0 - - - -
173B PHE* 3.6 35.3 - - + -
189B ASP* 3.0 24.9 - - - +
190B MET* 3.0 15.1 + - + +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 3.7 16.6 - - + +
100B CYS* 1.3 78.0 - - - +
102B ARG* 1.3 58.4 + - - +
103B ILE 4.1 9.2 - - - +
105B THR 3.6 13.3 + - - +
107B SER* 3.1 10.1 + - - -
108B PHE* 3.8 30.7 - - - +
111B ARG* 3.7 1.0 - - - +
121B PHE* 3.7 22.8 - - + -
124B PRO* 3.2 10.0 - - - +
125B LYS* 2.8 37.8 + - + +
127B GLU* 2.9 31.6 + - + -
129B PHE* 4.1 3.6 - - - -
173B PHE* 4.5 0.4 - - - -
188B VAL 3.8 4.3 - - - -
189B ASP* 3.7 19.0 + - + -
703B OK8 2.8 45.1 + - - -
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ALA 4.9 0.6 + - - -
317A GLU 4.8 1.0 + - - -
318A GLY* 3.5 40.4 + - - +
506A EDO 4.3 1.4 - - - -
101B ARG* 1.3 73.0 - - - +
103B ILE* 1.3 70.1 + - + +
120B LYS* 3.4 17.3 - - + -
121B PHE* 2.9 52.3 + - - -
122B TYR* 3.7 9.1 - - - +
123B PRO* 4.6 0.4 - - - +
124B PRO* 3.5 29.4 - - - +
173B PHE* 3.6 12.2 - - + -
174B GLU* 4.7 5.7 - - - +
177B GLU* 2.7 46.6 + - - +
186B THR* 5.9 1.6 - - + -
187B LEU 4.1 5.2 - - - +
188B VAL 2.9 11.8 + - - +
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 4.1 11.8 - - - +
102B ARG* 1.3 89.4 - - + +
104B ALA* 1.3 71.1 + - - +
105B THR* 3.3 4.7 + - - +
118B GLY* 3.6 26.0 - - - +
119B TYR 3.5 2.5 - - - -
120B LYS* 3.9 27.4 - - + -
121B PHE* 3.9 3.8 - - - -
186B THR* 3.8 29.2 - - + -
188B VAL* 3.3 32.1 + - + +
189B ASP* 4.6 0.7 - - - +
217B TRP* 4.5 23.8 - - + -
220B 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