Contacts of the strand formed by residues 116 - 121 (chain A) in PDB entry 4CEV
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.9 22.9 - - + -
109A VAL* 3.8 17.7 - - + -
110A ALA* 3.7 33.9 - - + +
113A TYR* 3.9 30.2 + - + +
114A GLU 4.1 0.4 - - - -
115A ARG* 1.3 72.6 - - - +
117A GLY* 1.3 69.2 + - - +
163A LYS 4.9 2.3 + - - +
164A ILE* 3.5 26.9 - - + +
168A HIS* 3.8 12.4 + - - +
218A THR* 4.3 0.9 - - - -
219A ASP* 3.7 0.6 + - - -
220A GLY* 3.3 27.6 - - - +
221A VAL 3.9 3.1 - - - +
222A HIS* 4.0 7.6 - - + +
265A THR* 4.3 2.7 - - - +
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ARG 3.6 3.0 + - - -
116A LEU* 1.3 75.8 - - - +
118A VAL* 1.3 67.0 + - - +
168A HIS 3.1 13.0 - - - -
214A LEU* 4.3 3.8 - - - -
218A THR* 3.6 17.0 - - - +
220A GLY 2.8 13.3 + - - -
221A VAL* 3.4 6.0 - - - -
222A HIS 2.9 24.1 + - - -
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.9 16.6 - - + -
116A LEU* 4.9 0.2 - - + -
117A GLY* 1.3 80.7 - - - +
119A ILE* 1.3 72.4 + - - +
120A TRP* 3.8 32.9 + - + +
143A LEU* 5.0 3.4 - - + -
164A ILE* 3.7 34.8 - - + -
168A HIS 2.8 10.4 + - - +
169A VAL* 3.5 12.1 - - + +
170A VAL* 2.9 27.2 + - - +
214A LEU* 4.2 3.4 - - - +
222A HIS* 3.4 18.6 - - + +
224A SER* 4.6 0.2 - - - -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL* 1.3 71.5 - - - +
120A TRP* 1.3 59.7 + - - +
121A TYR* 3.6 10.5 + - + +
170A VAL 3.4 4.5 - - - +
172A ILE* 4.1 23.6 - - + -
207A MET* 5.1 1.8 - - + -
210A THR* 4.1 14.6 - - + -
214A LEU* 3.5 27.6 - - + -
221A VAL* 4.0 3.8 - - + +
222A HIS 3.0 8.4 + - - +
223A LEU* 3.7 19.4 - - + +
224A SER* 2.9 29.1 + - - +
258A LEU* 3.6 36.8 - - + -
263A ILE* 4.8 2.7 - - + -
264A ILE* 4.1 12.1 - - + -
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Residues in contact with TRP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A HIS* 3.2 23.3 - + - -
102A ALA* 3.5 27.1 - - + -
106A LEU* 4.3 13.0 - - + -
118A VAL* 3.8 15.1 - - + -
119A ILE* 1.3 70.9 - - - +
121A TYR* 1.3 61.3 + - - +
122A ASP* 3.2 29.1 + - + +
124A HIS 4.0 1.8 - - - -
125A GLY 4.0 0.9 + - - -
126A ASP* 3.0 41.3 + - + +
142A PRO* 3.7 3.8 - - + -
143A LEU* 3.8 39.7 - - + -
169A VAL* 5.0 2.2 - - + -
170A VAL 2.8 11.0 + - - +
171A LEU* 3.4 31.7 - - + +
172A ILE 2.9 25.4 + - - +
224A SER* 3.6 27.6 - - - -
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Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE* 3.6 7.6 + - + +
120A TRP* 1.3 68.1 - - - +
122A ASP* 1.3 62.6 + - - +
172A ILE* 3.5 24.7 - - + -
203A MET* 3.6 12.4 - - + +
207A MET* 5.3 1.6 - - - -
223A LEU* 4.7 6.5 - - + -
224A SER 3.1 9.9 + - - +
225A LEU* 3.7 36.8 - - + -
226A ASP* 2.9 32.8 + - - +
229A GLY* 4.7 2.9 - - - -
230A LEU* 4.1 13.0 - - + -
246A LEU* 3.4 30.6 - - + +
250A GLU 4.0 0.2 + - - -
251A SER* 3.0 40.5 + - - -
254A ALA* 4.0 19.5 - - + -
255A MET* 4.4 7.0 - - + -
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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