Contacts of the strand formed by residues 192 - 199 (chain D) in PDB entry 1FTA
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 GLU 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B CYS* 5.6 0.5 - - - -
39B THR* 3.7 25.6 + - + +
42B LYS* 2.8 35.7 + - - -
12D THR* 3.5 37.1 - - + +
13D LEU* 4.8 0.5 + - - +
14D THR* 3.5 17.5 + - - -
186D LEU* 3.9 2.6 - - - +
187D ASP 2.8 31.2 + - - -
190D ILE* 3.5 22.4 - - + -
191D GLY* 1.3 77.4 - - - +
193D PHE* 1.3 61.8 + - - +
194D ILE* 3.5 13.1 - - + +
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Residues in contact with PHE 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D THR* 3.2 6.2 - - - -
13D LEU* 2.8 51.6 + - + +
38D CYS* 3.6 29.6 - - - -
41D VAL* 3.8 23.1 - - + -
42D LYS* 3.7 25.4 - - + -
171D THR* 4.2 8.7 - - + -
172D MET 4.5 0.2 - - - -
173D LEU* 3.8 28.7 - - + -
184D PHE* 3.9 17.7 - - + -
185D MET 3.3 4.3 - - - -
186D LEU* 3.7 38.8 - - + -
192D GLU* 1.3 74.5 + - - +
194D ILE* 1.3 60.7 + - - +
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Residues in contact with ILE 194 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C ILE* 4.0 7.2 - - + -
54C ALA* 4.0 30.1 - - + -
57C TYR* 3.9 28.3 - - + -
59C ILE* 5.6 1.3 - - + -
10D VAL* 4.2 15.0 - - + -
11D VAL 3.9 4.0 - - - +
12D THR* 4.6 4.9 - - + -
184D PHE* 3.1 4.0 - - - -
185D MET 2.9 34.8 + - - +
187D ASP* 4.5 3.1 - - + -
190D ILE* 4.6 0.4 - - + -
192D GLU* 3.5 39.9 - - + +
193D PHE* 1.3 74.5 - - - +
195D LEU* 1.3 62.0 + - - +
196D VAL* 3.0 23.1 + - + -
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Residues in contact with LEU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C TYR* 4.3 8.5 - - - +
11D VAL* 3.0 38.3 + - + +
16D PHE* 4.4 18.8 - - + -
182D ASN* 3.8 12.8 - - + +
183D CYS 3.6 6.3 - - - +
184D PHE* 3.6 35.0 - - + -
194D ILE* 1.3 71.0 - - - +
196D VAL* 1.3 60.6 - - - +
197D ASP 3.5 22.7 - - - +
198D LYS* 3.6 34.0 - - + -
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Residues in contact with VAL 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C ILE* 4.7 1.8 - - + -
57C TYR* 3.8 37.5 + - + +
172D MET* 3.8 28.0 - - + -
183D CYS* 3.3 14.1 + - + +
185D MET* 3.7 26.0 - - + +
194D ILE* 3.0 28.4 + - + +
195D LEU* 1.3 75.1 - - - +
197D ASP* 1.3 64.2 + - + +
198D LYS* 5.9 0.4 - - - -
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Residues in contact with ASP 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D ASN* 3.6 1.7 + - - -
183D CYS* 3.0 47.0 + - + +
195D LEU* 3.5 7.3 - - - +
196D VAL* 1.3 81.2 - - + +
198D LYS* 1.3 78.3 + - - +
200D VAL* 4.2 18.5 - - + +
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Residues in contact with LYS 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D ASN* 3.0 7.9 - - - +
195D LEU* 3.6 30.5 - - + -
196D VAL 6.5 0.2 - - - -
197D ASP* 1.3 84.8 + - - +
199D ASP* 1.3 76.1 + - + +
200D VAL* 3.3 3.3 + - - -
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Residues in contact with ASP 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D CYS 3.3 23.4 - - - +
180D GLY* 3.8 7.7 - - - -
181D VAL 3.2 11.8 + - - +
182D ASN* 2.9 16.2 - - - +
198D LYS* 1.3 76.7 - - + +
200D VAL* 1.3 64.2 + - - +
201D LYS* 3.8 24.4 + - - +
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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