Contacts of the strand formed by residues 171 - 176 (chain A) in PDB entry 1JTF
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 ALA 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A PHE* 4.0 9.0 - - + -
53A LEU* 3.3 38.6 - - + -
133A ILE 4.0 0.2 + - - -
134A ILE* 3.8 2.0 - - + -
135A LEU 3.3 19.3 + - - -
169A PRO* 3.3 11.0 - - - +
170A VAL* 1.3 86.3 - - + +
172A SER* 1.3 60.9 + - - +
212A SER 3.0 15.0 - - - +
213A ILE* 4.3 3.4 - - + -
214A TYR* 3.6 6.0 - - - -
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Residues in contact with SER 172 (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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49A PHE* 3.2 14.7 - - - -
135A LEU* 3.1 21.1 - - - -
164A ILE* 3.9 12.0 - - - +
169A PRO* 4.7 2.0 - - - -
171A ALA* 1.3 76.4 - - - +
173A SER* 1.3 58.4 + - - +
174A LEU* 4.1 12.5 - - - +
210A LEU 4.5 0.3 + - - -
211A LEU* 3.3 0.3 - - - -
212A SER* 2.7 36.3 + - - -
214A TYR* 2.9 29.0 + - - -
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Residues in contact with SER 173 (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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46A GLU* 5.5 4.1 - - - +
49A PHE* 3.6 27.8 - - - +
135A LEU 2.9 6.9 + - - +
136A ILE* 3.4 13.6 - - - +
137A SER 3.2 26.4 + - - +
172A SER* 1.3 73.3 - - - +
174A LEU* 1.3 63.5 + - - +
209A ARG* 4.1 14.4 + - - +
210A LEU 3.0 6.5 - - - -
211A LEU* 3.4 18.0 - - - +
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Residues in contact with LEU 174 (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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135A LEU* 4.4 16.6 - - + -
137A SER* 3.6 27.1 - - - -
160A GLN* 3.5 35.4 - - + +
161A ASN* 4.9 0.2 - - - +
164A ILE* 3.7 25.4 - - + -
172A SER* 4.1 11.2 - - - +
173A SER* 1.3 79.0 + - - +
175A LYS* 1.3 63.8 + - - +
176A TRP* 5.7 0.4 - - + -
191A PRO* 4.0 22.9 - - + -
209A ARG* 3.3 9.7 - - - +
210A LEU* 2.7 50.8 + - + +
212A SER* 5.7 0.7 - - - +
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Residues in contact with LYS 175 (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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41A LYS* 5.5 2.2 - - - +
137A SER 3.6 8.7 + - - +
138A ASP* 3.0 24.5 + - - +
139A VAL 3.2 27.4 - - - +
140A ARG* 4.4 12.7 - - - +
156A ASN* 6.1 0.9 - - + -
157A TYR* 3.4 14.0 - - + -
160A GLN* 3.4 27.1 + - - +
174A LEU* 1.3 71.9 - - - +
176A TRP* 1.3 60.3 + - - +
177A ARG* 4.2 0.7 - - + -
207A GLU* 3.1 27.9 + - + +
209A ARG* 3.5 24.8 - - - +
400A SAH 5.8 1.8 - - - -
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Residues in contact with TRP 176 (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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157A TYR* 3.4 39.3 - + - -
174A LEU* 3.4 6.5 + - + +
175A LYS* 1.3 75.8 - - - +
177A ARG* 1.3 74.4 + - - +
178A CYS* 3.7 17.9 - - + -
188A PHE* 3.7 22.0 - + - -
190A ILE* 3.5 37.2 - - + +
195A LYS* 4.2 12.5 - - + +
207A GLU* 3.4 2.5 - - - +
208A MET* 2.8 67.0 + - + +
210A LEU* 4.2 24.5 - - + +
224A VAL* 4.3 4.7 - - + -
232A TYR* 3.2 43.6 + + - -
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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