Contacts of the strand formed by residues 139 - 143 (chain D) in PDB entry 1EV2
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 PHE 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.0 24.9 - - + -
24D TYR 3.0 19.3 - - - -
25D CYS* 3.6 25.4 - - + -
32D LEU* 4.5 11.9 - - + -
103D TYR* 3.6 6.3 - - - -
104D ASN* 2.6 44.3 + - + +
105D THR* 5.3 0.2 - - - -
106D TYR* 4.3 24.5 - + + -
116D VAL* 3.4 39.9 - - + -
117D ALA* 4.2 8.7 - - - -
118D LEU* 4.3 15.0 - - + -
136D ALA 4.0 2.9 - - - -
137D ILE 3.3 17.9 - - - -
138D LEU* 1.3 75.1 - - - +
140D LEU* 1.3 60.9 - - - +
141D PRO* 4.1 0.9 - - - -
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Residues in contact with LEU 140 (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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23D LEU* 4.8 0.9 - - - -
24D TYR* 2.7 43.8 + - + +
102D ASN 3.9 10.5 - - - +
103D TYR* 4.2 9.6 - - + -
139D PHE* 1.3 75.1 - - - +
141D PRO* 1.3 68.4 - - + +
142D MET* 3.3 4.7 + - + +
168H ALA* 3.6 40.4 - - + +
169H VAL* 3.8 9.6 - - - +
170H PRO* 4.3 11.7 - - + -
249H VAL* 3.8 27.1 - - + -
251H ARG* 3.9 32.5 - - - +
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Residues in contact with PRO 141 (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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21D LYS* 4.4 22.9 - - + -
22D ARG 3.6 6.3 - - - +
23D LEU* 4.2 17.2 - - + -
104D ASN* 4.1 15.0 - - + +
106D TYR* 5.2 0.7 - - - +
139D PHE 3.9 5.8 - - - +
140D LEU* 1.3 83.6 - - + +
142D MET* 1.3 62.9 + - - +
249H VAL* 4.0 17.3 - - - +
251H ARG* 3.8 37.0 - - - +
283H ASP* 4.8 4.5 - - - +
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Residues in contact with MET 142 (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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21D LYS* 3.3 10.9 - - - +
22D ARG* 2.8 43.9 + - + +
24D TYR* 3.8 23.3 - - + -
31D PHE* 3.9 16.8 - - + -
140D LEU* 3.6 9.0 - - + +
141D PRO* 1.3 79.9 - - - +
143D SER* 1.3 65.6 + - - +
166H LEU* 5.6 1.8 - - + -
168H ALA* 3.9 15.3 - - + -
247H ASP* 3.6 39.9 - - + +
249H VAL* 4.2 20.2 - - + -
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Residues in contact with SER 143 (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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20D PRO 4.8 2.9 - - - -
21D LYS* 4.9 3.1 - - - +
22D ARG* 3.7 14.9 + - - +
142D MET* 1.3 79.4 - - - +
144D ALA* 1.3 58.8 + - - +
145D LYS* 2.9 27.1 + - - -
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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