Contacts of the strand formed by residues 220 - 225 (chain A) in PDB entry 2Y60
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 ILE 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A SER 4.6 1.1 - - - +
156A LEU* 4.0 19.7 - - + -
157A LEU* 4.1 16.4 - - + -
160A TYR* 3.7 39.9 - - + -
218A SER* 3.3 11.1 - - - -
219A LEU* 1.4 85.3 - - - +
221A THR* 1.3 61.0 + - - +
222A VAL* 4.0 17.7 - - + -
251A ILE* 4.3 2.9 - - + -
252A ASN 3.3 12.6 - - - +
253A CYS* 4.4 2.9 - - - -
257A MET* 3.9 16.2 - - + -
286A VAL* 2.9 49.6 + - + +
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Residues in contact with THR 221 (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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216A ASP* 2.7 30.3 + - - +
218A SER* 2.9 20.1 + - - -
220A ILE* 1.3 70.9 - - - +
222A VAL* 1.4 66.4 + - - +
223A LEU* 4.0 11.0 - - + -
250A LEU 3.5 1.4 - - - +
251A ILE* 3.3 10.0 - - - +
252A ASN* 2.8 36.8 + - - +
283A PRO* 4.4 11.2 - - + -
284A PHE 3.7 5.2 - - - +
285A PHE* 3.6 23.7 - - + -
1332A M8F 5.3 4.9 - - + -
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Residues in contact with VAL 222 (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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145A TYR* 5.4 0.2 + - - -
149A VAL* 3.8 17.0 - - + -
152A LEU* 4.0 13.0 - - + -
153A SER* 3.4 22.0 - - - +
156A LEU* 3.9 18.8 - - + -
220A ILE* 4.0 6.1 - - + -
221A THR* 1.4 77.1 - - - +
223A LEU* 1.3 58.3 + - - +
249A TYR* 3.7 23.1 - - + -
250A LEU 3.8 2.5 - - - -
251A ILE* 3.8 11.2 - - + -
282A LEU 4.0 2.1 - - - +
283A PRO 3.8 0.3 - - - -
284A PHE* 2.9 39.8 + - + +
286A VAL* 3.7 13.7 - - + -
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Residues in contact with LEU 223 (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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43A TYR* 5.4 0.3 - - - -
221A THR* 4.6 10.1 - - + -
222A VAL* 1.3 73.0 - - - +
224A TYR* 1.3 71.6 + - - +
225A GLN* 3.7 29.4 + - + +
231A LEU* 4.0 16.6 - - + -
248A GLY 4.1 0.5 - - - +
249A TYR* 3.4 10.1 - - - -
250A LEU* 2.8 55.7 + - + +
252A ASN* 5.9 0.7 - - - +
281A SER* 3.6 16.4 - - - +
282A LEU 3.9 1.3 - - - -
283A PRO* 3.5 33.0 - - + -
1332A M8F 4.2 17.0 - - + -
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Residues in contact with TYR 224 (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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51A VAL* 3.7 30.2 + - + -
52A GLN* 5.6 0.5 - - - -
54A LEU* 4.2 12.8 - - + -
55A SER* 3.5 23.0 + - - -
223A LEU* 1.3 74.2 - - - +
225A GLN* 1.3 85.9 + - - +
226A SER* 3.9 6.3 - - - -
246A ASP* 3.3 35.7 + - - +
248A GLY 4.3 11.0 - - - -
249A TYR* 3.8 19.2 - - + -
280A GLN* 3.8 20.0 + - + -
282A LEU* 2.8 61.4 + - + +
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Residues in contact with GLN 225 (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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223A LEU* 3.7 26.0 + - + +
224A TYR* 1.3 90.0 - - - +
226A SER* 1.3 72.2 + - - +
230A ASN* 2.9 36.2 + - - +
231A LEU* 3.5 16.9 - - - +
244A ALA* 6.0 2.1 - - + +
245A ASP 4.3 4.5 + - - +
246A ASP* 3.4 22.3 + - - +
250A LEU* 6.1 0.9 - - + -
279A ARG* 4.0 5.0 - - - +
280A GLN 3.4 8.5 - - - +
281A SER* 2.9 29.3 + - - +
1332A M8F 3.7 7.5 + - - -
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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