Contacts of the strand formed by residues 269 - 274 (chain A) in PDB entry 3THP
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 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 5.5 0.6 - - - +
130A PRO* 3.8 11.8 - - - +
261A ASP* 6.1 0.7 - - - +
262A PHE 3.6 3.8 - - - -
263A LYS* 4.3 20.6 - - + +
267A GLY 3.1 9.4 + - - +
268A ILE* 1.3 72.7 - - - +
270A VAL* 1.3 66.1 + - - +
271A PRO* 3.8 9.2 - - + +
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Residues in contact with VAL 270 (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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130A PRO* 3.3 28.7 - - + -
132A ALA 4.7 6.7 - - - +
133A LEU* 4.9 0.7 - - - -
134A PRO* 4.5 16.4 - - + -
261A ASP* 4.9 1.1 - - - -
262A PHE* 2.8 38.3 + - - +
268A ILE* 4.2 2.2 - - + -
269A ALA* 1.3 78.9 - - - +
271A PRO* 1.3 60.4 - - - +
272A VAL* 3.3 8.0 + - + -
290A TRP* 4.0 25.4 - - + -
312A ILE* 3.4 36.1 - - + -
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Residues in contact with PRO 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PRO* 5.8 0.2 - - + -
259A VAL* 5.3 10.0 - - + +
260A MSE 3.1 10.8 - - - +
261A ASP* 4.0 15.5 - - - +
269A ALA* 3.8 8.1 - - + +
270A VAL* 1.3 81.0 - - - +
272A VAL* 1.3 64.6 + - - +
273A MSE 4.1 0.2 + - - -
311A GLY 4.1 0.5 - - - +
312A ILE* 3.2 32.9 - - + +
313A ILE 4.1 11.7 + - - +
314A THR* 6.0 1.8 - - + -
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 3.9 17.9 - - + -
134A PRO* 5.0 0.2 - - + -
137A LEU* 3.8 11.7 - - + -
139A VAL* 4.2 17.0 - - + -
259A VAL* 3.2 11.9 - - - +
260A MSE 2.8 30.7 + - + +
262A PHE* 3.5 35.7 - - + -
270A VAL* 3.3 8.3 + - + +
271A PRO* 1.3 76.8 - - - +
273A MSE 1.3 66.7 + - - +
274A LEU* 3.8 24.2 + - + -
280A LEU* 4.9 1.1 - - + -
311A GLY* 4.1 9.9 - - - -
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Residues in contact with MSE 273 (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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139A VAL* 4.8 1.2 - - - +
257A GLU* 4.3 34.3 - - + +
258A ILE 3.9 9.6 - - - +
259A VAL* 4.0 15.7 - - + -
272A VAL* 1.3 79.4 - - - +
274A LEU* 1.3 70.2 + - - +
275A PRO* 3.0 18.0 - - + +
302A VAL* 4.5 25.1 - - + -
303A GLN 6.1 0.7 - - - +
309A LYS 3.8 18.4 - - - +
310A SER* 3.8 2.5 - - - -
311A GLY 3.2 34.7 + - - +
313A ILE* 4.6 5.6 - - + -
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Residues in contact with LEU 274 (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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139A VAL* 4.7 7.4 - - + -
253A SER* 4.1 12.2 + - - +
256A SER 4.5 1.0 - - - +
257A GLU* 3.7 1.7 - - - -
258A ILE* 2.9 44.8 + - + +
260A MSE 3.6 39.3 - - + -
272A VAL* 3.8 19.1 - - + +
273A MSE 1.3 72.4 - - - +
275A PRO* 1.3 67.7 - - - +
278A SER* 4.5 2.5 - - - +
280A LEU* 3.6 38.6 - - + -
328A ARG* 3.4 24.0 - - - +
403A AKG 4.5 0.7 - - - +
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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