Contacts of the strand formed by residues 258 - 263 (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 ILE 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A TYR* 5.9 5.4 - - + -
253A SER* 5.4 0.2 - - - -
256A SER 4.6 0.4 - - - +
257A GLU* 1.3 79.0 - - - +
259A VAL* 1.3 80.1 + - - +
260A MSE 5.5 0.7 - - + -
273A MSE 3.9 3.2 - - - +
274A LEU* 2.9 43.5 + - + +
294A ILE* 3.8 16.6 - - + -
300A ASP* 4.6 5.2 - - - -
325A ARG* 3.2 51.8 - - + +
328A ARG* 3.3 49.4 - - + +
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Residues in contact with VAL 259 (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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258A ILE* 1.3 88.3 - - - +
260A MSE 1.3 63.2 + - - +
261A ASP* 4.8 5.1 - - - +
271A PRO* 5.3 9.9 - - + -
272A VAL 3.2 14.6 - - - +
273A MSE 4.0 19.7 - - + -
293A GLY 4.2 0.7 - - - +
294A ILE* 4.0 13.9 - - - +
295A THR* 4.9 4.0 + - + +
297A ARG* 5.0 5.4 - - - +
300A ASP* 2.8 38.8 - - + +
301A THR 4.7 11.2 - - - +
302A VAL* 5.0 1.8 - - + -
325A ARG* 3.7 10.8 + - - +
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Residues in contact with MSE 260 (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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235A ILE* 5.1 0.4 - - + -
258A ILE* 4.4 1.1 + - + -
259A VAL* 1.3 75.0 - - - +
261A ASP* 1.3 63.9 + - - +
262A PHE* 3.8 24.7 + - + -
270A VAL 3.7 1.2 - - - +
271A PRO* 3.1 6.1 - - - +
272A VAL* 2.8 35.8 + - + +
274A LEU* 3.6 32.2 - - + +
280A LEU* 3.8 19.5 - - + -
292A HIS* 3.6 31.9 - - + -
293A GLY* 3.2 14.6 - - - +
294A ILE* 4.1 16.8 - - + -
403A AKG 3.3 32.5 - - + +
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Residues in contact with ASP 261 (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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259A VAL* 4.8 2.5 - - - +
260A MSE 1.3 72.3 - - - +
262A PHE* 1.3 61.9 + - - +
263A LYS* 3.4 31.9 + - + +
269A ALA* 6.1 0.7 - - - +
270A VAL 4.3 2.0 - - - -
271A PRO* 4.0 19.2 - - - +
291A THR 3.0 11.3 - - - +
292A HIS* 3.2 0.7 - - - -
293A GLY 2.8 28.1 + - - +
295A THR* 3.3 38.5 + - - +
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Residues in contact with PHE 262 (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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134A PRO* 4.3 8.7 - - + -
137A LEU* 3.5 37.0 - - + -
260A MSE 3.9 24.9 - - + -
261A ASP* 1.3 74.1 - - - +
263A LYS* 1.3 61.9 + - - +
269A ALA* 3.6 0.2 - - - -
270A VAL 2.8 37.9 + - - +
272A VAL* 3.5 34.3 - - + -
280A LEU* 4.4 7.0 - - + -
282A MSE 4.2 10.5 - - - -
286A SER* 4.9 4.7 - - - -
290A TRP* 3.6 25.4 - - + -
291A THR 3.0 9.6 - - - -
292A HIS* 3.3 35.2 - + + -
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Residues in contact with LYS 263 (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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237A ALA* 4.1 21.8 - - - +
261A ASP* 3.4 35.8 + - + +
262A PHE* 1.3 80.1 - - - +
264A HIS* 1.3 67.4 + - - +
265A PRO* 3.7 1.2 - - - +
267A GLY 5.7 1.6 - - - +
268A ILE 3.4 6.3 - - - +
269A ALA* 4.3 17.9 - - + -
290A TRP* 3.5 7.3 - - - -
291A THR* 3.0 36.3 + - - +
293A GLY* 5.5 0.2 - - - -
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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
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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