Contacts of the strand formed by residues 147 - 151 (chain A) in PDB entry 3TIN
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 TRP 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.2 49.4 - - + -
98A TYR* 3.7 26.9 - + - -
131A PHE* 4.0 14.1 - + - -
134A SER 4.5 7.4 - - - -
135A PHE* 3.5 21.1 - + - -
138A LYS* 4.1 21.1 - - + -
145A ASN* 3.1 28.1 + - - -
146A VAL* 1.3 77.5 - - - +
148A ILE* 1.3 61.4 + - - +
162A ILE* 3.3 11.8 - - - +
163A SER 2.8 30.2 + - - +
164A SER* 5.5 0.7 - - - -
169A LEU* 4.2 9.0 - - + -
182A ILE* 3.4 23.1 - - + -
183A GLN* 3.3 12.8 - - - -
184A LYS* 3.2 29.8 - - + -
185A TYR* 4.2 2.2 - - - -
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Residues in contact with ILE 148 (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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147A TRP* 1.3 76.3 - - - +
149A ALA* 1.3 70.5 + - - +
150A LYS* 3.9 30.9 + - + +
160A ILE* 4.6 14.4 - - + -
161A LEU 3.0 13.9 - - - +
162A ILE* 3.9 25.1 - - + -
169A LEU* 5.5 0.2 - - - -
181A VAL 3.4 2.4 - - - +
182A ILE* 3.3 6.0 - - - -
183A GLN* 2.8 56.8 + - + +
185A TYR* 4.5 13.5 - - + -
702A ADP 4.4 22.2 - - + +
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Residues in contact with ALA 149 (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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148A ILE* 1.3 71.8 - - - +
150A LYS* 1.3 59.9 - - - +
160A ILE* 3.2 30.0 - - - +
161A LEU* 2.7 27.6 + - + +
169A LEU* 4.4 14.2 - - + +
173A ILE* 6.0 4.3 - - + -
180A HIS* 4.6 15.9 - - + +
181A VAL 3.7 4.3 - - - -
182A ILE* 4.5 10.1 - - + +
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Residues in contact with LYS 150 (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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74A LYS* 4.7 20.8 - - + +
148A ILE* 4.0 22.3 - - + +
149A ALA* 1.3 78.5 - - - +
151A SER* 1.3 62.0 + - - +
159A GLY 4.6 0.2 - - - -
160A ILE* 4.0 17.1 - - + +
180A HIS* 2.9 10.7 - - - +
181A VAL* 2.8 56.1 + - + +
183A GLN* 4.2 15.9 - - + +
330A ILE* 4.6 7.8 - - - +
702A ADP 3.2 62.5 + - - -
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Residues in contact with SER 151 (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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74A LYS* 3.8 16.7 + - - +
150A LYS* 1.3 73.8 - - - +
152A SER* 1.3 70.5 + - - +
153A SER 4.7 0.2 - - - -
154A GLY* 3.8 29.3 + - - -
159A GLY 3.4 21.1 + - - -
160A ILE* 4.9 1.9 - - - +
178A GLN* 4.3 7.4 - - - -
180A HIS* 3.2 30.2 - - - -
702A ADP 5.6 1.6 + - - -
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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