Contacts of the strand formed by residues 111 - 116 (chain X) in PDB entry 2CE2
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 MET 111 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78X PHE* 3.2 14.1 - - + +
80X CYS* 3.9 20.0 - - - -
97X ARG* 3.4 47.6 - - + +
100X ILE* 3.0 40.2 - - + -
101X LYS* 4.5 1.6 - - + +
109X VAL* 2.7 26.7 + - + +
110X PRO* 1.3 77.4 - - - +
112X VAL* 1.3 73.2 + - - +
139X ILE* 3.5 24.2 - - + +
140X PRO* 3.4 16.5 - - - +
159X LEU* 3.9 1.5 - - - +
162X GLU* 4.4 5.8 + - - +
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Residues in contact with VAL 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X PHE 3.1 5.1 + - - +
79X LEU* 3.7 20.2 - - + +
80X CYS* 2.9 28.9 + - - +
111X MET* 1.3 82.2 - - - +
113X LEU* 1.3 74.8 - - - +
114X VAL* 4.1 5.8 - - + -
139X ILE* 4.0 4.9 - - - -
140X PRO* 3.6 16.4 - - + +
142X ILE* 4.2 22.7 - - + -
155X ALA* 4.3 2.9 - - - +
158X THR* 4.1 12.3 - - + -
159X LEU* 3.7 33.4 - - + +
162X GLU* 4.5 1.8 - - + -
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Residues in contact with LEU 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80X CYS* 3.5 17.7 - - + +
82X PHE* 3.8 22.0 - - + -
93X ILE* 4.0 24.7 - - + -
112X VAL* 1.3 77.3 - - - +
114X VAL* 1.3 58.1 + - - +
130X ALA* 3.4 34.8 - - + +
133X LEU* 4.3 10.5 - - + -
134X ALA* 3.7 17.0 - - + +
137X TYR* 5.4 3.1 - - + -
139X ILE* 3.8 12.2 - - + +
140X PRO 2.9 12.7 + - - +
141X TYR* 3.4 15.3 - - + -
142X ILE 3.0 25.5 + - - -
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Residues in contact with VAL 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X LEU* 4.1 16.2 - - + -
79X LEU* 4.1 26.0 - - + -
80X CYS 2.9 11.8 + - - +
81X VAL* 3.4 11.6 - - + -
82X PHE* 3.0 34.6 + - - +
112X VAL* 4.1 5.2 - - + +
113X LEU* 1.3 79.2 - - - +
115X GLY* 1.3 61.2 + - - +
142X ILE 3.2 4.3 - - - +
144X THR* 3.3 36.1 - - + +
155X ALA* 4.0 22.2 - - + -
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Residues in contact with GLY 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X PHE* 3.5 26.2 - - - -
84X ILE* 3.7 8.0 - - - +
114X VAL* 1.3 70.3 - - - +
116X ASN* 1.3 62.9 + - - -
118X SER 4.7 0.5 + - - -
141X TYR* 3.5 13.0 - - - -
142X ILE 3.1 8.3 + - - -
143X GLU* 3.2 9.2 - - - +
144X THR* 2.9 25.6 + - - +
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Residues in contact with ASN 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X VAL 2.9 26.9 + - - +
15X GLY* 3.7 8.5 + - - -
19X LEU* 3.7 9.5 - - + +
81X VAL* 4.1 11.9 - - + -
82X PHE 2.9 12.7 + - - +
83X ALA* 3.5 0.5 - - - -
84X ILE* 3.0 23.0 + - - +
114X VAL 3.8 0.2 - - - -
115X GLY* 1.3 72.6 - - - +
117X LYS* 1.3 80.8 + - - +
118X SER 3.4 0.4 - - - -
144X THR* 2.8 28.4 + - - +
146X ALA* 3.3 9.6 + - - +
180X GDP 3.0 35.1 + - - +
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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