Contacts of the strand formed by residues 97 - 103 (chain B) in PDB entry 3CB4
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 GLY 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B ASN 3.5 4.0 + - - -
7B PHE* 3.3 22.8 - - - -
8B SER* 3.3 4.3 + - - -
95B CYS* 3.5 9.6 - - - +
96B GLU* 1.3 81.9 - - - +
98B ALA* 1.3 61.7 + - - +
124B LEU* 3.8 7.3 - - - +
125B GLU 3.1 16.8 - - - -
180B ILE* 3.8 13.1 - - - +
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Residues in contact with ALA 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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7B PHE* 4.5 1.1 - - - -
8B SER* 3.0 22.9 - - - +
10B ILE* 3.8 27.4 - - + -
92B LEU* 4.6 6.3 - - + -
97B GLY* 1.3 75.6 - - - +
99B LEU* 1.3 63.1 + - - +
100B LEU 3.6 0.3 + - - -
119B ALA* 4.9 4.7 - - + -
124B LEU* 4.8 2.9 - - + -
125B GLU 2.9 6.6 + - - +
126B VAL* 3.4 7.7 - - + +
127B VAL* 2.8 26.0 + - - +
180B ILE* 4.0 3.8 - - - +
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Residues in contact with LEU 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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7B PHE* 3.9 28.0 - - + -
8B SER 2.8 11.8 + - - +
9B ILE* 3.5 10.7 - - + +
10B ILE* 2.9 29.2 + - - +
20B LEU* 3.8 18.6 - - + -
24B ILE* 4.2 7.6 - - + -
98B ALA* 1.3 74.1 - - - +
100B LEU* 1.3 59.2 + - - +
101B VAL* 3.5 6.9 + - + -
127B VAL* 3.3 33.9 - - + +
129B VAL* 4.2 3.4 - - + -
172B VAL* 3.6 31.2 - - + -
176B LEU* 4.3 19.1 - - + -
180B ILE* 4.8 0.9 - - + -
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Residues in contact with LEU 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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10B ILE* 3.6 20.9 - - + +
98B ALA 3.6 2.6 + - - -
99B LEU* 1.3 71.0 - - - +
101B VAL* 1.3 56.5 + - - +
102B VAL* 3.8 20.9 + - + +
108B VAL* 5.5 3.4 - - + -
112B THR* 4.1 21.8 - - - +
113B LEU* 6.4 0.2 - - + -
116B CYS* 3.7 30.5 - - - -
126B VAL* 3.9 19.5 - - + -
127B VAL 2.8 10.4 + - - +
128B PRO* 3.4 6.8 - - + +
129B VAL* 2.7 33.5 + - - +
147B ILE* 4.4 14.1 - - + -
151B VAL* 4.2 18.6 - - + -
153B ILE* 5.4 0.7 - - + -
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Residues in contact with VAL 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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9B ILE* 3.9 22.9 - - + -
10B ILE 3.0 12.6 + - - +
11B ALA* 3.8 23.9 - - + +
12B HIS 4.8 1.6 + - - -
20B LEU* 3.6 35.7 - - + +
99B LEU* 4.1 6.7 - - + +
100B LEU* 1.3 76.1 - - - +
102B VAL* 1.3 64.4 + - - +
103B ASP 4.3 0.7 + - - +
112B THR* 5.8 1.9 - - - +
129B VAL* 3.5 9.2 - - + +
131B ASN* 3.7 33.9 - - + +
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Residues in contact with VAL 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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100B LEU* 4.0 24.9 - - + +
101B VAL* 1.3 79.2 - - - +
103B ASP* 1.3 60.5 + - - +
104B ALA* 3.2 1.0 + - - -
107B GLY 3.4 34.3 - - - +
108B VAL* 4.1 11.2 - - + +
129B VAL 2.7 12.9 + - - +
130B LEU* 3.4 5.6 - - + +
131B ASN* 2.8 31.0 + - - -
143B VAL* 3.6 20.6 - - + -
147B ILE* 3.9 27.4 - - + -
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Residues in contact with ASP 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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13B ILE* 4.8 12.9 - - + +
101B VAL* 4.3 0.8 + - - +
102B VAL* 1.3 71.7 - - - +
104B ALA* 1.3 59.2 + - - +
105B GLY* 2.8 31.2 + - - -
106B GLN* 3.5 29.8 + - + +
107B GLY* 3.0 26.8 + - - +
131B ASN* 3.5 13.0 - - - +
132B LYS* 3.8 33.9 - - + +
135B LEU* 4.2 8.5 - - - +
143B VAL* 4.1 0.3 - - - +
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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