Contacts of the strand formed by residues 187 - 191 (chain E) in PDB entry 4GDK
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 187 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ILE* 3.2 26.6 + - + -
186E PRO* 1.3 75.5 - - - +
188E ARG* 1.3 71.3 + - - +
189E ILE* 3.8 18.2 - - + -
199E ILE 3.7 16.6 - - - -
200E GLN* 3.5 19.2 - - + +
201E LYS 3.1 37.2 - - - -
203E PHE* 3.9 10.5 - - + -
218E LEU* 3.7 41.3 - - + -
222E VAL* 4.0 29.6 - - + -
264E PHE* 3.8 2.7 - - - -
265E LEU* 3.4 20.9 - - + +
267E ILE* 4.6 3.4 - - + -
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Residues in contact with ARG 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D SER* 4.5 7.9 + - - -
113D ASP* 5.5 3.4 + - - -
114D GLN* 3.3 23.6 + - - +
81E TYR* 5.8 3.6 - - - -
124E HIS* 5.7 2.4 + - - -
128E CYS* 4.5 16.7 - - - +
131E GLU* 3.4 22.0 + - - -
187E PHE* 1.3 80.4 - - - +
189E ILE* 1.3 62.5 + - - +
190E TYR* 3.2 32.3 + - + +
198E PHE* 3.5 39.4 - - + -
199E ILE 3.5 4.0 - - - -
200E GLN* 3.1 15.7 + - + +
264E PHE* 3.6 27.4 - - + -
265E LEU 3.1 7.8 + - - -
266E HIS* 3.5 16.0 - - - +
267E ILE 2.9 24.3 + - - -
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Residues in contact with ILE 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E PHE* 3.8 18.2 - - + -
188E ARG* 1.3 73.2 - - - +
190E TYR* 1.3 66.0 + - - +
191E GLN* 4.3 2.4 + - + +
198E PHE* 3.2 5.8 - - - -
199E ILE* 2.8 48.0 + - + +
218E LEU* 4.9 1.8 - - + -
219E LEU* 3.8 24.5 - - + -
222E VAL* 3.7 29.4 - - + -
223E CYS* 4.3 17.7 - - + -
267E ILE* 3.5 17.7 - - + +
269E ILE* 3.7 27.8 - - + -
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Residues in contact with TYR 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E TYR* 3.5 37.5 - + - -
85E LEU* 3.4 34.9 - - + +
89E LEU* 3.9 26.6 - - + +
188E ARG* 3.2 41.1 + - + -
189E ILE* 1.3 74.5 - - - +
191E GLN* 1.3 62.6 + - - +
197E PRO 3.6 17.0 - - - +
198E PHE* 3.8 11.4 - + + -
266E HIS* 2.7 36.8 + - + -
267E ILE 2.8 14.1 + - - +
268E SER* 4.7 0.2 - - - -
269E ILE* 2.9 30.5 + - - +
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Residues in contact with GLN 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E LEU* 4.4 4.8 - - - +
189E ILE* 4.3 2.8 + - + +
190E TYR* 1.3 76.7 - - - +
192E THR* 1.3 65.2 + - - +
193E THR* 4.2 19.0 + - + +
194E THR* 3.1 41.9 - - + +
196E ARG 4.7 0.9 - - - +
197E PRO 4.9 3.7 + - - +
199E ILE* 5.7 2.4 - - - +
223E CYS* 4.0 18.3 - - - -
225E SER* 4.1 15.0 + - - -
236E ASN* 4.7 6.9 + - - +
269E ILE* 3.6 38.7 + - + +
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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