Contacts of the strand formed by residues 191 - 197 (chain L) in PDB entry 6IAP
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 VAL 191 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149L LYS 3.7 2.6 - - - +
150L VAL* 3.6 2.6 - - - -
151L ASP* 2.9 51.0 + - - +
152L ASN* 4.4 7.6 - - + +
190L LYS* 1.4 91.6 - - + +
192L TYR* 1.3 63.9 + - - +
193L ALA* 5.4 4.5 - - + +
208L SER* 5.5 5.2 - - - -
209L PHE 3.5 4.7 - - - +
210L ASN* 3.6 21.8 - - - +
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Residues in contact with TYR 192 (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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117L ILE* 3.8 8.7 - - - +
132L VAL* 4.4 6.7 - - + -
148L TRP* 4.9 2.5 - - + -
149L LYS 4.0 2.5 - - - -
150L VAL* 3.5 35.5 - - + +
179L LEU* 4.1 15.0 - - + -
181L LEU* 4.7 7.1 - - + +
185L ASP 3.6 2.9 + - - -
186L TYR* 2.6 62.7 + + - -
189L HIS* 3.3 32.3 - - - +
190L LYS 3.3 14.1 - - - -
191L VAL* 1.3 72.1 - - - +
193L ALA* 1.3 60.1 + - - +
208L SER* 3.3 2.0 - - - -
209L PHE* 3.0 56.1 + + + -
211L ARG* 4.4 1.8 - - + -
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Residues in contact with ALA 193 (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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117L ILE* 4.2 0.9 - - - -
147L GLN 3.9 0.2 - - - +
148L TRP* 3.3 12.6 - - - -
149L LYS* 2.8 47.1 + - + +
191L VAL* 5.6 4.0 - - + -
192L TYR* 1.3 71.7 - - - +
194L CYS* 1.3 61.6 + - - +
195L GLU* 4.1 0.6 + - - -
206L THR* 3.9 18.8 - - + -
207L LYS 3.3 6.1 - - - +
208L SER* 3.3 24.9 - - - -
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Residues in contact with CYS 194 (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 VAL* 4.1 10.5 - - - -
117L ILE* 3.9 14.3 - - - +
134L CYS* 2.0 55.2 - - + -
146L VAL* 3.8 5.6 - - + -
147L GLN 3.2 9.0 - - - +
148L TRP* 3.9 11.4 - - + -
193L ALA* 1.3 73.3 - - - +
195L GLU* 1.3 58.7 + - - +
196L VAL* 3.9 2.2 + - - +
205L VAL 3.6 2.4 - - - +
206L THR* 4.5 1.8 - - - -
207L LYS* 2.9 34.7 + - - +
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Residues in contact with GLU 195 (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 LYS 3.4 2.1 - - - +
146L VAL* 3.3 2.9 - - - -
147L GLN* 2.8 56.4 + - + +
149L LYS* 3.2 38.8 + - + -
193L ALA 4.1 0.6 - - - -
194L CYS* 1.3 71.1 - - - +
196L VAL* 1.3 63.0 + - - +
197L THR 4.1 0.2 + - - -
204L PRO* 4.3 18.6 - - + +
205L VAL 3.3 4.9 - - - +
206L THR* 3.3 29.2 + - + +
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Residues in contact with VAL 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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113L PRO* 3.9 10.8 - - + -
115L VAL* 3.9 25.1 - - + -
134L CYS* 4.5 1.6 - - - -
136L LEU* 3.7 48.2 - - + -
145L LYS 3.3 3.4 - - - +
146L VAL* 4.1 9.9 - - + -
194L CYS 4.5 1.1 - - - +
195L GLU* 1.3 75.9 - - - +
197L THR* 1.3 65.7 - - - +
198L HIS* 4.7 0.4 - - + -
201L LEU* 3.9 21.5 - - + +
204L PRO* 3.2 8.3 - - - +
205L VAL* 2.7 37.4 + - + +
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Residues in contact with THR 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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144L ALA* 3.5 2.6 - - - +
145L LYS* 2.7 60.4 + - + -
195L GLU 5.5 0.4 - - - -
196L VAL* 1.3 70.2 - - - +
198L HIS* 1.3 64.5 + - - +
201L LEU* 4.8 0.4 - - - -
204L PRO* 3.5 26.9 - - - +
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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