Contacts of the strand formed by residues 293 - 300 (chain B) in PDB entry 1P7L
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 ARG 293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B TYR* 3.8 18.0 + - - +
126B ALA 3.3 15.0 - - - +
127B THR* 4.1 12.3 - - - +
286B VAL* 3.9 3.4 - - - -
291B ALA* 3.3 1.5 - - - -
292B ASP* 1.3 84.3 - - + +
294B CYS* 1.3 65.4 + - - +
314B THR* 3.3 10.9 - - - +
315B PHE* 3.3 67.3 + - + +
317B THR* 3.1 18.4 + - + +
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Residues in contact with CYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TYR* 4.1 2.5 - - - -
126B ALA 3.2 27.7 + - - -
282B ALA* 3.7 20.5 - - - +
285B ILE* 3.7 36.3 - - + -
286B VAL* 4.3 3.6 - - + +
291B ALA* 4.5 4.3 - - + -
293B ARG* 1.3 77.5 - - - +
295B GLU* 1.3 58.6 + - - +
296B ILE* 4.4 9.6 - - - -
312B VAL* 5.2 3.6 - - - -
313B GLU 2.9 13.7 - - - +
314B THR* 3.5 19.5 - - + -
315B PHE* 3.8 3.3 - - - -
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 5.4 0.9 - - - -
123B PHE* 4.1 12.9 - - + -
124B GLY 3.3 14.8 - - - +
125B TYR* 3.5 12.3 - - + -
254B MET 4.8 0.5 - - - +
255B ALA* 3.2 11.2 - - + -
256B ARG* 2.6 68.0 + - - +
294B CYS* 1.3 73.4 - - - +
296B ILE* 1.3 62.4 + - - +
311B MET* 3.8 3.7 - - + +
312B VAL* 3.5 1.7 - - - -
313B GLU* 2.7 45.5 + - + +
315B PHE* 3.7 21.3 - - + -
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B PHE* 3.3 9.6 - - - -
124B GLY 2.9 28.4 + - - +
278B ALA* 4.1 31.4 - - + +
281B VAL* 3.5 32.3 - - + -
282B ALA* 4.4 3.4 - - + -
285B ILE* 4.5 2.0 - - + -
294B CYS* 4.1 12.3 - - - -
295B GLU* 1.3 77.4 - - - +
297B GLN* 1.3 72.0 + - - +
298B VAL* 4.8 8.7 - - + +
310B ILE* 5.2 3.6 - - + -
311B MET 3.4 4.0 - - - +
312B VAL* 3.5 35.4 - - + -
329B VAL* 4.5 11.7 - - + -
335B LEU* 6.2 1.8 - - + -
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU 4.4 3.6 + - - -
5A PHE* 3.6 20.3 - - - -
6A THR* 3.4 20.7 + - - +
121B LEU* 3.3 25.6 - - + +
122B MET 3.2 11.0 - - - +
123B PHE* 3.1 41.4 - - + -
296B ILE* 1.3 80.0 - - - +
298B VAL* 1.3 67.3 + - - +
309B SER* 3.6 6.3 + - - +
310B ILE* 3.1 6.8 + - - +
311B MET* 3.0 51.0 + - + +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.2 3.9 - - - +
122B MET* 2.7 60.1 + - + +
274B ALA* 4.2 11.4 - - + +
278B ALA* 4.9 5.4 - - + -
296B ILE* 4.9 6.7 - - + -
297B GLN* 1.3 77.3 - - - +
299B SER* 1.3 59.4 + - - +
300B TYR* 3.8 17.7 - - + +
307B PRO* 5.1 1.8 - - + -
309B SER* 3.0 6.5 - - - +
310B ILE* 3.8 27.1 - - + -
335B LEU* 3.9 26.9 - - + -
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Residues in contact with SER 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A THR* 3.2 25.5 + - - +
167A GLN* 3.9 1.1 - - - -
120B GLY 2.9 12.3 - - - -
121B LEU* 3.9 4.9 - - - -
297B GLN* 5.4 0.2 - - - -
298B VAL* 1.3 74.7 - - - +
300B TYR* 1.3 67.7 + - - +
307B PRO* 3.7 3.6 - - - +
308B THR* 2.4 45.9 + - - -
309B SER* 3.0 29.8 + - - -
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Residues in contact with TYR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN* 2.6 26.7 + - - -
116B ALA* 3.8 19.7 - - + -
118B ASP 3.9 6.5 - - - +
119B GLN* 3.1 3.9 - - - -
120B GLY 2.6 23.4 + - - +
122B MET* 3.8 11.9 - - - -
270B VAL* 3.7 24.2 - - + -
274B ALA* 3.2 33.8 - - + +
298B VAL* 3.8 17.4 - - + +
299B SER* 1.3 74.2 - - - +
301B ALA* 1.3 60.9 + - - +
304B VAL 4.8 2.2 - - - -
305B ALA 4.7 1.1 - - - -
306B GLU 5.0 0.2 - - - -
307B PRO* 3.7 25.1 - - + -
308B THR* 3.6 6.1 - - - +
335B LEU* 2.7 42.2 + - - +
337B PRO* 4.2 10.8 - - + -
340B LEU* 3.6 4.8 - - + +
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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