Contacts of the strand formed by residues 202 - 209 (chain B) in PDB entry 4YCG
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 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 5.6 3.6 - - - +
109B ILE* 4.0 18.9 - - + +
110B LEU 3.5 15.3 - - - +
111B ILE* 4.0 32.5 - - + +
151B ASP* 3.4 2.3 - - - +
152B VAL* 3.3 36.7 + - + +
155B ASP* 3.1 29.4 + - + +
191B TRP* 3.2 17.2 - - - -
199B ASN* 5.4 3.8 - - - +
200B LYS* 3.9 15.9 - - - +
201B ASN* 1.3 80.0 - - - +
203B LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 3.4 2.6 - - - +
110B LEU* 2.7 58.3 + - + -
112B PHE* 3.9 8.7 - - + -
127B LEU* 4.0 20.0 - - + -
149B VAL* 4.1 13.7 - - + -
150B TYR 3.1 19.7 - - - +
151B ASP* 4.2 1.8 - - - -
152B VAL* 3.8 7.0 - - - -
169B LEU* 4.3 9.9 - - + -
184B VAL* 4.9 2.0 - - + -
187B ALA* 4.9 1.3 - - + -
191B TRP* 3.6 14.1 - - + -
202B LYS* 1.3 79.8 - - - +
204B GLU* 1.3 55.8 + - - +
205B VAL* 4.2 5.6 - - + -
231B PHE* 3.6 30.3 - - + -
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Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LYS* 5.3 0.2 - - - -
108B HIS 3.2 13.2 - - - +
109B ILE* 4.0 14.4 - - + +
149B VAL* 3.2 1.6 - - - -
150B TYR* 2.6 45.3 + - - +
152B VAL* 3.5 15.8 - - + +
160B ASP* 3.7 10.0 - - - +
161B GLN* 2.7 58.6 + - - +
163B THR 5.4 0.2 - - - +
166B LYS* 3.4 20.0 + - + +
203B LEU* 1.3 72.6 - - - +
205B VAL* 1.3 65.6 + - - +
206B THR* 3.8 11.2 - - + +
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Residues in contact with VAL 205 (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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106B GLN 3.7 1.7 - - - +
108B HIS* 2.6 44.9 + - + +
110B LEU* 4.0 23.3 - - + -
127B LEU* 4.1 10.3 - - + -
129B LEU* 3.9 13.7 - - + -
147B MET* 4.9 5.2 - - - -
148B VAL 3.4 8.5 - - - +
149B VAL* 3.8 22.7 - - + -
182B LEU* 5.6 0.4 - - + -
203B LEU* 4.2 2.2 - - + -
204B GLU* 1.3 74.8 - - - +
206B THR* 1.3 70.9 + - - +
207B VAL* 4.4 5.4 - - + -
219B ILE* 3.7 25.6 - - + -
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Residues in contact with THR 206 (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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105B PHE* 3.9 26.7 - - + -
106B GLN 3.1 7.2 - - - +
107B LYS* 4.7 2.9 - - + -
147B MET* 3.1 6.4 - - - +
148B VAL* 2.7 58.1 + - - +
150B TYR* 3.8 9.8 + - + +
161B GLN* 3.9 13.7 - - + +
204B GLU* 3.8 23.8 - - + +
205B VAL* 1.3 78.2 - - - +
207B VAL* 1.3 62.6 + - - +
208B GLN* 4.1 1.0 + - - +
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Residues in contact with VAL 207 (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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105B PHE* 3.3 6.0 - - - +
106B GLN* 2.9 35.3 + - + +
108B HIS* 4.4 3.6 - - + -
131B VAL* 6.0 0.2 - - + -
146B SER 3.8 6.5 - - - +
147B MET* 4.1 7.0 - - + -
174B ILE* 4.6 9.2 - - + -
205B VAL* 4.4 5.2 - - + -
206B THR* 1.3 76.7 - - - +
208B GLN* 1.3 62.2 + - - +
209B SER 3.7 2.1 + - - -
217B LEU* 3.4 34.1 - - + +
218B ASP* 3.6 30.1 - - - +
219B ILE* 3.9 26.7 - - + -
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Residues in contact with GLN 208 (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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104B PRO* 2.9 36.1 + - - +
105B PHE* 3.3 20.1 - - + -
145B GLY* 3.5 2.1 - - - -
146B SER* 2.6 56.3 + - - +
147B MET* 5.5 0.2 - - - -
206B THR* 4.1 2.1 + - - -
207B VAL* 1.3 73.4 - - - +
209B SER* 1.3 84.7 + - - +
210B HIS* 3.8 7.1 - - + -
217B LEU* 4.5 1.2 - - - +
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Residues in contact with SER 209 (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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104B PRO 5.1 0.4 + - - -
105B PHE* 5.5 0.6 - - - +
207B VAL* 3.7 5.0 + - - +
208B GLN* 1.3 92.0 + - - +
210B HIS* 1.3 70.9 + - - +
213B SER* 3.7 7.3 + - - -
214B CYS 2.4 30.5 + - - -
215B ASP* 4.6 6.0 - - - -
217B LEU* 3.9 23.5 - - - +
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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