Contacts of the strand formed by residues 161 - 167 (chain B) in PDB entry 3ME9
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 LYS 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B SER* 4.8 10.3 - - - +
159B GLY 2.9 22.4 + - - +
160B ASP* 1.3 75.0 - - - +
162B VAL* 1.3 64.8 + - - +
177B LEU* 4.6 4.3 - - + -
178B ALA 3.4 4.9 - - - +
179B GLU* 3.4 23.3 + - + -
195B ILE* 3.8 26.5 - - + -
212B PRO* 4.0 1.2 - - - +
213B LEU* 3.1 43.4 + - + +
282B ARG* 4.4 19.5 - - - +
283B TYR* 6.2 0.7 - - + -
294B UNX 3.1 17.1 - - - -
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ALA* 4.3 7.2 - - + -
160B ASP 4.2 0.4 - - - +
161B LYS* 1.3 81.2 - - - +
163B ALA* 1.3 63.8 + - - +
164B ALA* 4.4 1.8 - - + -
177B LEU* 3.6 7.3 - - - +
178B ALA* 2.9 53.1 + - + +
180B VAL* 3.5 25.1 - - + -
192B VAL* 4.3 14.4 - - + -
210B VAL* 3.6 26.5 - - + -
211B ILE 3.3 12.8 - - - +
212B PRO* 4.0 7.0 - - + -
213B LEU* 3.8 8.0 - - - +
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B VAL* 1.3 74.4 - - - +
164B ALA* 1.3 58.9 + - - +
175B TRP* 3.4 16.8 - - + -
176B ILE 3.4 5.8 - - - -
210B VAL* 3.4 4.2 - - - -
211B ILE* 2.9 44.8 + - + +
213B LEU* 3.7 6.6 - - + +
235B LEU* 5.6 0.2 - - + -
244B PHE* 3.6 31.9 - - + -
285B VAL* 4.5 7.2 - - + -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B VAL* 4.4 4.5 - - + -
163B ALA* 1.3 74.9 - - - +
165B ARG* 1.3 59.5 + - - +
166B VAL* 3.4 5.7 + - + -
174B GLN 3.4 0.2 - - - +
175B TRP* 3.3 4.0 - - - -
176B ILE* 2.8 46.2 + - + +
178B ALA* 4.0 11.0 - - + -
192B VAL* 4.0 15.5 - - + -
205B LEU* 3.6 23.6 - - + -
209B ARG 3.3 5.6 - - - +
210B VAL* 4.7 1.8 - - + +
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLY* 5.8 5.9 + - - -
164B ALA* 1.3 70.0 - - - +
166B VAL* 1.3 60.4 + - - +
173B GLU* 3.6 39.1 + - + +
174B GLN 3.6 8.3 - - - +
175B TRP* 3.4 39.4 - - + +
205B LEU* 3.8 7.0 - - - +
208B ARG 5.9 0.2 - - - -
209B ARG* 2.8 62.4 + - + +
288B LYS 4.9 1.5 + - - -
289B GLU* 2.8 41.0 + - - -
290B PRO* 4.5 9.3 - - - +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ALA* 4.0 4.3 - - + +
165B ARG* 1.3 74.1 - - - +
167B LYS* 1.3 72.2 + - - +
168B ALA* 3.6 3.9 + - + +
172B ASP 3.5 2.8 - - - +
173B GLU* 3.6 2.6 - - - -
174B GLN* 2.9 37.1 + - + +
176B ILE* 3.7 36.8 - - + -
203B HIS* 3.8 38.8 - - + +
205B LEU* 4.6 11.4 - - + -
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Residues in contact with LYS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ARG 3.9 2.2 + - - -
166B VAL* 1.3 76.7 - - - +
168B ALA* 1.3 72.6 + - - +
169B VAL 6.0 0.2 - - - -
171B GLY* 3.8 27.6 - - - +
172B ASP 3.5 3.1 - - - -
173B GLU* 3.4 27.2 + - - +
205B LEU* 5.5 1.8 - - - +
209B ARG* 4.0 14.5 - - - +
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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