Contacts of the strand formed by residues 316 - 323 (chain B) in PDB entry 1EQR
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 GLY 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B ALA* 5.5 1.4 - - - +
310B PRO* 3.2 20.0 - - - +
311B ALA 5.1 0.9 - - - +
313B ASP* 3.4 16.1 + - - +
314B PRO 3.3 1.4 - - - +
315B LYS* 1.3 79.9 - - - +
317B ARG* 1.3 62.3 + - - +
397B ASP 3.3 13.2 - - - -
398B ASN* 4.1 1.8 - - - -
399B LYS* 3.1 15.7 - - - -
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU 3.1 26.3 + - - -
277B ARG* 3.0 26.3 + - - +
292B LEU* 4.3 8.1 - - - +
294B ASP* 3.3 40.3 + - - +
296B ALA* 5.1 4.0 - - + -
310B PRO* 3.6 3.1 + - - +
316B GLY* 1.3 74.6 - - - +
318B VAL* 1.3 64.7 + - - +
319B ALA* 3.8 21.0 - - - +
396B ALA* 3.4 2.4 - - - -
397B ASP 2.9 32.8 + - - +
399B LYS* 4.0 33.0 - - + +
402B VAL* 3.5 34.9 - - + +
403B ALA* 4.7 6.9 - - - +
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ASP* 3.5 7.7 + - - +
295B VAL* 3.1 33.7 + - + +
296B ALA* 4.0 14.1 - - - +
299B LEU* 3.5 27.1 - - + -
307B PHE* 4.0 13.0 - - + +
310B PRO* 4.2 0.4 - - + -
311B ALA* 3.9 29.6 - - + +
317B ARG* 1.3 80.1 - - - +
319B ALA* 1.3 59.4 + - - +
394B PHE* 4.4 11.9 - - + -
395B GLY 3.4 4.3 - - - +
396B ALA* 3.7 22.4 - - + -
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Residues in contact with ALA 319 (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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292B LEU* 4.2 14.6 - - + -
293B THR 3.4 4.0 - - - -
317B ARG* 3.8 19.4 - - - +
318B VAL* 1.3 74.6 - - - +
320B ALA* 1.3 61.5 + - - +
393B PHE 3.6 0.7 - - - +
394B PHE* 3.2 8.6 - - - +
395B GLY 2.8 33.9 + - - +
402B VAL* 3.5 25.6 - - + -
406B MET* 4.2 10.3 - - + +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU 3.7 2.1 - - - +
292B LEU* 3.3 5.2 - - - -
293B THR* 2.6 44.4 + - - +
295B VAL* 4.0 8.7 - - + -
318B VAL 4.0 0.2 + - - -
319B ALA* 1.3 75.3 - - - +
321B LEU* 1.3 60.5 + - - +
322B ARG 3.9 0.9 + - - -
384B THR* 3.7 24.5 - - + -
392B ILE* 4.1 4.0 - - + -
393B PHE 3.3 4.0 - - - -
394B PHE* 3.9 24.9 - - + -
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Residues in contact with LEU 321 (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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290B MET* 4.0 26.9 - - + -
291B GLU 3.7 17.5 - - - +
292B LEU* 3.7 14.4 - - + -
319B ALA 4.0 0.6 + - - -
320B ALA* 1.3 71.9 - - - +
322B ARG* 1.3 61.4 + - - +
323B VAL* 3.7 19.1 + - + +
391B MET 3.3 1.9 - - - +
392B ILE* 3.2 4.5 - - - -
393B PHE* 2.6 40.9 + - + +
406B MET* 3.5 24.9 - - + -
409B LEU* 4.3 13.5 - - + +
410B ARG* 3.7 33.2 - - + +
413B VAL* 4.8 2.9 - - + -
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Residues in contact with ARG 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B MET* 3.4 14.9 - - - +
291B GLU 4.3 6.1 + - - +
293B THR* 5.9 0.7 - - - +
320B ALA 3.9 2.4 + - - -
321B LEU* 1.3 74.2 - - - +
323B VAL* 1.3 60.3 + - - +
324B PRO* 3.3 27.4 - - - +
384B THR* 3.1 32.2 + - + +
385B ALA* 3.4 17.6 + - - +
386B ALA* 4.5 0.7 - - - -
387B GLN* 3.7 18.6 - - - +
390B ASP* 2.7 37.5 + - + +
391B MET 3.3 4.7 - - - -
392B ILE* 3.8 21.5 - - + -
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B MET* 3.5 15.7 - - + -
321B LEU* 3.9 14.4 - - + +
322B ARG* 1.3 75.2 - - - +
324B PRO* 1.3 66.6 - - + +
326B GLY* 3.0 23.3 + - - +
329B LEU* 5.5 0.9 - - + -
390B ASP* 4.4 1.3 - - - -
391B MET* 2.8 27.0 + - + +
393B PHE* 3.8 30.3 - - + -
413B VAL* 3.9 9.0 - - + -
417B LEU* 3.5 31.2 - - + -
419B LEU* 4.9 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
------------------------------------------------------------
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