Contacts of the strand formed by residues 183 - 189 (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 SER 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ARG* 3.7 8.4 + - - -
104A CYS* 4.0 6.1 - - - -
105A TYR 3.4 12.1 - - - -
106A LEU* 3.7 6.7 - - - -
146A TYR* 4.4 0.4 - - - -
181A LEU 3.6 0.8 + - - -
182A ALA* 1.3 76.2 - - - +
184A VAL* 1.3 62.7 + - - +
185A VAL* 4.5 0.7 - - - +
283A PRO 3.8 0.5 - - - +
284A PHE* 3.3 8.1 - - - -
285A PHE* 2.9 47.8 + - - +
287A ASN* 4.2 0.4 - - - +
1332A M8F 2.7 31.6 + - - -
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Residues in contact with VAL 184 (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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103A PHE 3.9 0.5 - - - +
104A CYS* 3.3 4.3 - - - -
105A TYR* 3.0 69.6 + - + +
145A TYR* 4.3 22.2 - - + -
146A TYR* 3.8 21.5 - - + -
183A SER* 1.3 71.7 - - - +
185A VAL* 1.3 67.4 + - - +
186A LEU* 3.7 20.0 - - + -
282A LEU 5.7 1.1 - - - -
283A PRO 3.4 7.4 - - - +
284A PHE* 3.6 23.8 - - + -
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Residues in contact with VAL 185 (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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91A TYR* 6.1 1.3 - - + -
102A SER* 3.8 17.7 - - - +
103A PHE 3.5 8.5 - - - +
104A CYS* 4.2 18.8 - - + -
183A SER* 4.5 0.7 - - - +
184A VAL* 1.3 80.3 - - - +
186A LEU* 1.3 64.6 + - - +
187A ILE* 3.6 21.8 - - + -
281A SER 3.5 0.3 - - - +
282A LEU* 3.3 10.7 - - - +
283A PRO* 3.0 37.3 + - + +
285A PHE* 3.9 26.0 - - + -
1332A M8F 4.2 15.5 - - + +
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Residues in contact with LEU 186 (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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54A LEU* 4.7 7.4 - - + -
58A THR* 3.8 29.4 - - + +
61A PHE* 4.5 3.8 - - + -
62A HIS* 2.9 23.7 + - + +
102A SER* 3.2 0.9 - - - -
103A PHE* 2.8 44.8 + - + +
105A TYR* 4.2 10.3 - - + +
138A PHE* 3.8 33.9 - - + -
142A ALA* 5.4 1.6 - - + -
145A TYR* 5.5 0.7 - - + -
184A VAL* 3.7 24.0 - - + -
185A VAL* 1.3 72.1 - - - +
187A ILE* 1.4 58.8 + - - +
282A LEU* 3.7 19.5 - - + -
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Residues in contact with ILE 187 (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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62A HIS* 3.6 5.5 - - - -
100A VAL* 3.3 33.9 - - + -
101A GLU 3.6 4.5 - - - +
102A SER* 3.7 4.9 - - - -
185A VAL* 3.6 22.7 - - + -
186A LEU* 1.4 71.5 - - - +
188A ARG* 1.3 59.0 + - - +
189A TYR* 3.7 18.2 - - + -
280A GLN* 3.5 6.9 - - - -
281A SER* 2.9 42.5 + - - +
282A LEU* 3.7 1.6 - - - +
283A PRO* 3.9 8.5 - - + -
1332A M8F 3.5 45.1 - - - +
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Residues in contact with ARG 188 (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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62A HIS* 3.5 45.4 + - + +
63A MET* 3.6 26.3 - - - +
70A LYS* 5.4 2.8 - - - +
100A VAL* 3.6 3.5 - - - +
101A GLU* 2.8 63.6 + - + +
187A ILE* 1.3 73.6 - - - +
189A TYR* 1.3 61.8 + - - +
190A PRO* 3.6 20.6 - - - +
191A TYR 5.3 1.6 + - - -
192A LEU* 6.2 0.2 - - - +
278A GLU* 2.8 43.0 + - - +
279A ARG 3.9 5.2 - - - +
280A GLN* 6.5 0.2 - - + -
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Residues in contact with TYR 189 (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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100A VAL* 3.9 29.0 - - + +
187A ILE* 3.7 19.5 - - + -
188A ARG* 1.3 71.0 - - - +
190A PRO* 1.3 68.0 - - + +
195A TYR* 5.0 6.5 - - - +
210A SER* 3.6 31.9 + - - -
211A PHE* 4.2 7.4 - - - +
272A VAL* 4.0 8.2 - - + +
275A VAL 5.9 1.1 - - - +
277A ALA 3.2 4.3 - - - +
278A GLU* 3.4 1.6 - - - +
279A ARG* 2.8 84.0 + - + +
281A SER* 4.1 7.6 - - - -
1332A M8F 2.7 39.7 + - - -
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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