Contacts of the strand formed by residues 111 - 115 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C PRO* 3.1 28.8 - - - +
15D TRP* 4.6 8.3 - - + -
78D HIS* 3.9 39.0 - - + +
81D PRO* 4.9 2.5 - - + -
82D PHE* 3.9 12.1 - - + -
96D ALA* 4.4 7.9 - - + -
97D SER 3.4 15.9 - - - +
98D HIS* 4.0 18.2 - - + -
99D LEU* 4.4 3.0 - - - +
105D CYS 5.6 0.2 - - - +
106D HIS* 4.0 13.2 - - - +
107D ASN 3.5 18.8 - - - +
108D PRO* 3.3 17.8 + - + +
109D LEU 3.4 1.2 + - - -
110D HIS* 1.3 87.8 - - - +
112D CYS* 1.3 64.1 + - - +
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Residues in contact with CYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C THR* 4.3 4.9 - - + -
152C ALA 3.4 15.0 - - - +
153C GLY* 4.3 6.3 - - - -
154C PRO* 4.5 0.9 - - + -
82D PHE* 3.6 10.9 - - - -
95D THR 3.3 2.9 - - - +
96D ALA* 3.4 3.3 - - - -
97D SER* 2.7 38.2 + - - -
99D LEU* 3.5 24.0 - - + -
111D LEU* 1.3 79.8 - - - +
113D TRP* 1.3 59.3 + - - +
114D GLU* 3.1 37.2 - - - -
122D ARG* 4.2 5.4 - - - -
136D VAL* 4.7 4.5 - - + -
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Residues in contact with TRP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C THR* 3.4 2.8 - - - +
151C VAL* 3.0 35.3 + - + +
152C ALA* 3.0 18.1 + - + +
79D THR* 4.0 33.4 - - + -
82D PHE* 3.2 57.4 - + + -
83D LEU* 6.2 0.7 - - + -
85D GLU* 4.1 12.5 - - + +
86D PRO 2.7 27.8 + - - -
87D ASP* 4.2 7.4 - - + +
94D CYS* 3.4 42.2 - - + +
95D THR* 3.1 33.0 - - - -
96D ALA* 3.7 4.7 - - - -
112D CYS* 1.3 68.9 - - - +
114D GLU* 1.3 61.8 + - - +
15N A 4.3 0.9 - - - -
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C THR* 2.7 34.4 + - + +
151C VAL* 4.7 1.3 - - - +
89D ILE* 5.7 0.2 - - - -
94D CYS* 4.0 7.6 - - - +
95D THR* 3.0 28.6 + - - +
97D SER* 2.4 39.4 + - - -
112D CYS* 3.1 10.5 - - - -
113D TRP* 1.3 76.0 - - - +
115D SER* 1.3 76.8 + - - +
118D ASP* 3.8 10.4 - - + +
119D ASN* 3.6 9.6 - - - +
122D ARG* 2.8 29.1 + - - -
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Residues in contact with SER 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ALA 6.2 0.4 - - - -
150C THR* 5.7 0.2 - - - +
89D ILE* 4.7 9.8 - - - +
92D LYS* 4.1 35.1 - - - +
93D THR 3.6 11.2 - - - -
94D CYS* 4.4 4.1 - - - +
95D THR* 4.6 1.1 + - - -
114D GLU* 1.3 81.0 - - - +
116D ALA* 1.3 65.1 + - - +
117D ASP* 3.8 5.4 + - - +
118D ASP* 2.7 34.7 + - - -
119D ASN* 3.2 19.8 + - - +
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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