Contacts of the strand formed by residues 172 - 176 (chain A) in PDB entry 1TF5
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 ILE 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 3.6 30.7 - - + +
118A ALA* 3.9 10.5 - - + -
124A VAL* 3.6 5.6 - - + +
126A VAL* 3.9 15.5 - - + -
145A PHE* 3.3 46.7 - - + -
150A LEU* 4.2 14.6 - - + -
151A THR 3.1 7.0 + - - +
152A VAL* 3.5 5.9 - - + -
153A GLY 2.7 30.8 + - - -
170A ALA* 3.5 2.6 - - - +
171A ASP* 1.3 85.2 - - + +
173A THR* 1.3 63.0 + - - +
174A TYR* 4.0 17.3 - - + -
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Residues in contact with THR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL 2.8 14.7 + - - -
125A HIS* 3.3 17.7 - - + +
126A VAL 2.9 25.4 + - - -
153A GLY 3.4 6.7 - - - +
155A ASN* 4.2 15.7 - - + -
167A ALA 2.8 32.1 + - - +
168A TYR* 3.8 23.1 + - + -
170A ALA 4.3 2.9 + - - -
171A ASP 5.3 0.2 - - - -
172A ILE* 1.3 76.0 - - - +
174A TYR* 1.3 72.5 + - - +
175A SER* 3.9 3.5 + - - -
180A LEU* 5.7 0.2 - - + -
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Residues in contact with TYR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 5.6 0.8 - - + +
110A SER* 5.0 5.6 + - - -
111A THR* 5.1 0.2 - - - +
126A VAL* 3.3 35.1 - - + +
128A THR* 6.0 2.0 - - + -
134A ALA* 3.7 20.4 - - - +
137A ASP* 3.3 32.3 - - + -
138A ALA* 3.7 31.6 - - + -
141A MET* 3.2 26.1 - - + +
145A PHE* 3.6 14.3 - + - -
152A VAL* 4.0 15.7 - - + -
153A GLY 2.8 8.9 + - - +
154A LEU* 3.6 7.2 - - + +
155A ASN* 2.9 26.0 + - - +
172A ILE* 4.0 19.1 - - + -
173A THR* 1.3 73.3 - - - +
175A SER* 1.3 61.8 + - - +
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A HIS* 6.1 0.2 - - - -
126A VAL 3.0 7.0 + - - -
127A VAL* 3.4 4.1 - - - -
128A THR* 2.9 30.7 + - - +
134A ALA* 4.3 4.9 - - - +
155A ASN* 3.1 36.4 + - - -
173A THR* 3.9 3.6 + - - -
174A TYR* 1.3 78.0 - - - +
176A THR* 1.3 75.6 + - - +
179A GLU* 3.7 3.6 - - - +
180A LEU* 3.5 28.1 - - - +
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Residues in contact with THR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 3.6 4.0 - - - -
128A THR* 3.3 11.0 - - + +
129A VAL 4.4 4.3 - - - +
130A ASN* 3.4 38.4 - - - +
131A GLU* 3.5 19.5 - - + +
134A ALA* 4.5 0.9 - - + -
155A ASN 4.7 1.0 + - - +
156A LEU* 6.0 0.2 - - + -
175A SER* 1.3 81.8 + - - +
177A ASN* 1.3 65.1 - - - +
178A ASN* 3.8 8.1 + - - +
179A GLU* 3.3 26.5 + - - +
180A LEU* 3.2 23.2 + - - +
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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
------------------------------------------------------------
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