Contacts of the strand formed by residues 93 - 99 (chain B) in PDB entry 3C5C
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 ALA 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ASN 3.3 3.8 + - - -
23B LEU* 3.4 18.4 - - + -
24B ALA 3.0 23.6 + - - -
91B ALA* 3.4 5.8 - - - +
92B HIS* 1.3 82.3 - - - +
94B PHE* 1.3 69.2 + - - +
128B PRO* 3.3 22.0 - - + +
130B LEU* 5.0 0.9 - - + -
179B ALA* 3.8 29.6 - - + +
183B ALA* 4.6 0.7 - - + -
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Residues in contact with PHE 94 (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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24B ALA* 3.4 17.5 - - + +
26B LEU* 3.8 15.3 - - + -
87B TYR* 3.6 32.8 - + - -
88B LEU* 4.3 13.7 - - + -
91B ALA* 3.6 26.5 - - + -
93B ALA* 1.3 76.2 - - - +
95B LEU* 1.3 62.4 + - - +
96B VAL* 4.6 1.1 - - + -
116B LEU* 3.7 40.8 - - + -
127B ILE* 3.7 27.6 - - + -
128B PRO 2.9 15.9 + - - +
129B ALA* 3.3 3.7 - - + -
130B LEU* 2.7 38.1 + - - +
179B ALA* 5.6 0.2 - - - -
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Residues in contact with LEU 95 (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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23B LEU* 5.1 4.0 - - + +
24B ALA 3.0 7.2 + - - +
25B ILE* 3.2 37.1 - - + +
26B LEU* 2.8 33.4 + - - +
36B LEU* 6.0 1.1 - - + -
94B PHE* 1.3 73.0 - - - +
96B VAL* 1.3 55.9 + - - +
97B VAL* 4.0 0.9 - - + -
130B LEU* 3.3 26.5 - - + -
132B LEU* 3.9 27.6 - - + -
175B VAL* 4.3 4.9 - - + +
176B PHE* 3.9 32.3 - - + -
179B ALA* 3.7 29.4 - - + -
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Residues in contact with VAL 96 (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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26B LEU* 3.5 16.6 - - + +
94B PHE* 4.6 2.5 - - + -
95B LEU* 1.3 74.6 - - - +
97B VAL* 1.3 57.9 + - - +
109B SER* 3.7 38.1 - - - +
112B TYR* 3.8 16.2 - - + -
113B LEU* 4.0 14.6 - - + -
116B LEU* 3.9 28.3 - - + -
129B ALA* 4.8 1.8 - - + -
130B LEU 2.8 12.9 + - - +
131B LEU* 3.4 17.0 - - + +
132B LEU 2.8 28.8 + - - +
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Residues in contact with VAL 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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25B ILE* 3.6 30.5 - - + -
26B LEU 2.8 12.9 + - - +
27B GLY* 3.5 18.5 - - - -
28B ARG 4.2 1.7 + - - -
31B ALA* 3.6 19.8 - - + +
33B LYS* 4.1 11.0 - - + +
36B LEU* 3.8 22.0 - - + -
95B LEU 4.4 2.2 - - - +
96B VAL* 1.3 76.3 - - - +
98B TYR* 1.3 64.2 + - - +
105B SER* 4.3 0.7 + - - +
109B SER* 4.3 5.6 - - - -
132B LEU* 3.4 18.2 - - + +
134B ASN* 3.7 28.0 - - + -
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Residues in contact with TYR 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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31B ALA* 4.0 6.3 - - - -
97B VAL* 1.3 73.1 - - - +
99B SER* 1.3 67.2 + - - +
100B VAL* 4.2 9.9 - - + -
105B SER* 3.1 33.4 - - - +
106B PHE* 3.5 31.8 - + + -
109B SER* 3.8 15.5 - - - -
131B LEU* 3.8 22.7 - - + -
132B LEU 2.8 19.9 + - - +
133B GLY* 3.5 17.5 - - - -
134B ASN* 2.6 37.4 + - - +
144B VAL* 4.1 13.2 - - + +
145B THR 4.8 0.2 + - - -
149B GLY* 3.5 9.9 + - - -
160B PHE* 3.0 27.7 - - - -
162B GLU* 4.6 3.1 + - - -
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Residues in contact with SER 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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30B GLY 5.0 0.4 - - - -
31B ALA* 4.3 5.6 - - - +
98B TYR* 1.3 80.9 - - - +
100B VAL* 1.3 58.9 + - - +
101B ASP* 2.2 30.9 + - - -
102B SER* 3.0 38.6 + - - +
105B SER* 3.0 11.0 + - - -
134B ASN 3.7 4.5 - - - -
135B LYS* 3.1 34.4 - - - +
144B VAL* 4.5 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