Contacts of the strand formed by residues 111 - 115 (chain B) in PDB entry 1EVW
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 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A PRO* 3.2 27.2 - - - +
15B TRP* 4.6 9.0 - - + -
78B HIS* 3.9 28.5 - - + +
81B PRO* 4.8 3.1 - - + -
82B PHE* 3.9 12.8 - - + -
96B ALA* 4.8 5.4 - - + -
97B SER 3.3 16.4 - - - +
98B HIS* 3.7 31.2 - - + +
99B LEU* 4.4 3.5 - - - +
105B CYS* 6.1 0.4 - - - -
106B HIS 4.0 12.6 - - - +
107B ASN 3.5 17.7 - - - +
108B PRO* 3.2 18.6 + - + +
109B LEU 3.4 1.2 + - - -
110B HIS* 1.3 86.7 - - + +
112B CYS* 1.3 65.9 + - - +
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Residues in contact with CYS 112 (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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150A THR* 4.1 6.5 - - + -
152A ALA 3.4 13.9 - - - +
153A GLY* 4.3 5.6 - - - -
154A PRO* 4.8 2.2 - - + -
82B PHE* 3.6 10.7 - - - -
95B THR 3.2 3.6 - - - +
96B ALA* 3.2 3.3 - - - -
97B SER* 2.7 53.8 + - - -
99B LEU* 3.4 31.0 - - + -
111B LEU* 1.3 79.0 - - - +
113B TRP* 1.3 58.4 + - - +
114B GLU* 3.5 19.5 + - - -
122B ARG* 4.2 3.1 - - - -
136B VAL* 4.9 2.5 - - + -
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Residues in contact with TRP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A THR* 3.2 5.5 - - - +
151A VAL* 2.7 46.4 + - + -
152A ALA* 2.8 20.5 + - + +
79B THR* 4.2 21.1 - - + -
82B PHE* 3.6 45.5 - + + -
83B LEU* 6.2 0.9 - - + -
85B GLU* 3.8 17.2 - - + +
86B PRO 2.5 28.7 + - - -
87B ASP* 4.8 7.4 - - + -
94B CYS* 3.5 34.2 - - + +
95B THR 2.9 32.3 - - - -
96B ALA* 3.6 5.8 - - + -
112B CYS* 1.3 70.4 - - - +
114B GLU* 1.3 55.1 + - - +
15M A 3.5 14.8 - - - -
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Residues in contact with GLU 114 (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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149A ALA 5.4 0.2 - - - -
150A THR* 2.6 42.5 + - + +
151A VAL* 4.5 2.7 - - - +
94B CYS* 4.1 5.2 - - - -
95B THR* 3.0 29.2 + - - +
97B SER* 2.9 28.7 + - - -
112B CYS* 3.5 8.3 - - - -
113B TRP* 1.3 76.3 - - - +
115B SER* 1.3 75.2 + - - +
118B ASP* 3.8 10.2 - - + +
119B ASN* 3.2 15.3 + - - +
122B ARG* 2.7 35.2 + - - -
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Residues in contact with SER 115 (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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149A ALA* 5.6 1.7 + - - -
89B ILE* 4.7 11.3 - - - +
92B LYS* 4.2 33.5 - - - +
93B THR 3.7 11.2 - - - -
94B CYS* 4.5 2.1 - - - +
95B THR* 4.7 1.1 - - - -
114B GLU* 1.3 80.1 - - - +
116B ALA* 1.3 63.3 + - - +
117B ASP* 3.6 5.7 + - - +
118B ASP* 2.8 33.4 + - - +
119B ASN* 3.1 20.1 + - - +
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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