Contacts of the strand formed by residues 193 - 199 (chain L) in PDB entry 2IG2
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 TYR 193 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119L LEU* 4.9 0.4 - - - -
134L LEU* 3.7 22.4 - - + -
150L TRP* 5.0 3.8 - + + -
151L LYS 3.5 8.1 - - - -
152L ALA* 3.5 23.0 - - + +
157L VAL* 4.5 6.1 - - + -
180L LEU* 3.7 23.6 - - + -
182L LEU* 3.7 23.2 - - + +
186L GLN* 3.8 9.7 + - - +
187L TRP* 3.7 41.5 - + - -
190L HIS* 3.7 29.7 + - + -
192L SER* 1.3 75.5 + - - +
194L SER* 1.3 65.3 + - - +
207L THR* 3.4 0.2 - - - -
208L VAL* 2.7 52.3 + - + +
210L PRO* 5.3 2.5 - - + -
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Residues in contact with SER 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119L LEU* 4.6 0.9 - - - -
149L ALA 3.6 0.9 - - - +
150L TRP* 3.8 7.3 - - - -
151L LYS* 2.9 48.6 + - - +
192L SER* 4.1 3.3 + - - -
193L TYR* 1.3 77.7 + - - +
195L CYS* 1.3 60.4 + - - +
196L GLN* 3.5 5.8 + - - +
205L GLU* 3.9 21.0 + - - -
206L LYS 3.3 8.7 - - - -
207L THR* 2.9 26.1 + - - +
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Residues in contact with CYS 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117L VAL* 4.1 7.4 - - + +
119L LEU* 4.2 15.9 - - + +
136L CYS* 2.0 52.3 - - + -
148L VAL* 3.6 24.9 - - - -
149L ALA 3.8 3.6 - - - -
150L TRP* 4.3 10.3 - - + -
194L SER* 1.3 69.5 - - - +
196L GLN* 1.3 63.0 + - - +
197L VAL* 3.8 1.7 + - - -
204L VAL 3.5 4.5 - - - +
205L GLU* 3.9 0.4 - - - -
206L LYS 3.0 27.6 + - - +
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Residues in contact with GLN 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L VAL* 3.5 1.2 - - - +
149L ALA* 2.6 60.1 + - + +
151L LYS* 3.4 41.0 + - + +
194L SER* 3.5 2.1 + - - +
195L CYS* 1.3 74.3 - - - +
197L VAL* 1.3 57.9 + - - +
198L THR* 4.3 3.9 + - - -
203L THR* 3.9 19.8 - - + +
204L VAL 3.4 4.9 - - - -
205L GLU* 3.3 38.5 - - + +
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Residues in contact with VAL 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L PRO* 4.7 6.9 - - + +
117L VAL* 3.3 45.1 - - + -
138L ILE* 3.9 28.3 - - + -
146L VAL* 4.2 15.0 - - + -
147L THR 3.1 21.3 - - - +
148L VAL* 4.0 8.5 - - + -
195L CYS* 4.4 1.3 - - - +
196L GLN* 1.3 76.6 - - - +
198L THR* 1.3 59.0 + - - +
199L HIS* 4.0 1.2 + - - -
202L SER 3.7 0.3 - - - +
203L THR* 3.4 1.1 - - - +
204L VAL* 2.8 44.0 + - + +
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Residues in contact with THR 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L ALA 4.5 0.9 - - - +
146L VAL 3.8 0.5 - - - -
147L THR* 2.7 52.1 + - - +
149L ALA* 6.1 0.9 - - - +
196L GLN* 5.0 3.8 + - - -
197L VAL* 1.3 70.2 - - - +
199L HIS* 1.3 60.8 + - - +
200L GLU 4.2 0.7 - - - -
201L GLY* 4.2 14.6 - - - +
202L SER 3.3 9.2 - - - +
203L THR* 2.9 34.3 + - - +
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Residues in contact with HIS 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L LYS* 4.8 2.7 - - + -
113L ALA 3.3 14.3 + - - -
114L ASN* 4.3 10.7 + - - -
115L PRO* 3.6 33.8 - - + +
141L PHE* 4.0 4.0 - + + -
142L TYR 3.1 28.5 + - - -
143L PRO* 2.7 39.1 + - + +
145L ALA 3.5 19.1 - - - -
146L VAL* 3.7 17.0 - - + -
197L VAL 4.0 0.2 - - - -
198L THR* 1.3 74.6 - - - +
200L GLU* 1.4 77.3 + - + +
201L GLY 3.5 0.2 - - - -
202L SER* 2.7 21.9 + - - +
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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