Contacts of the strand formed by residues 316 - 323 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C PRO* 3.5 8.9 - - - +
313C ASP* 2.6 17.5 + - - +
314C PRO* 4.3 1.7 - - - +
315C LYS* 1.3 81.3 - - - +
317C ARG* 1.3 68.2 + - - +
397C ASP 3.2 15.0 - - - -
398C ASN* 3.7 1.8 - - - -
399C LYS* 3.5 19.2 + - - +
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Residues in contact with ARG 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C GLU* 3.2 23.8 + - - +
277C ARG* 2.9 30.3 + - - +
292C LEU* 4.2 7.5 - - - +
294C ASP* 2.8 39.8 + - - +
296C ALA* 4.8 6.3 - - + -
310C PRO* 3.3 11.6 + - - +
316C GLY* 1.3 76.9 - - - +
318C VAL* 1.3 63.0 + - - +
319C ALA* 3.8 14.3 - - - +
395C GLY 3.3 9.4 - - - +
396C ALA* 3.6 0.7 - - - -
397C ASP 3.0 19.7 + - - +
399C LYS* 4.0 28.0 + - + +
402C VAL* 3.4 35.4 - - + +
403C ALA* 4.3 13.7 - - - +
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Residues in contact with VAL 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C ASP* 3.6 5.2 - - - -
295C VAL* 2.9 47.7 + - + +
296C ALA* 3.7 15.0 + - - +
299C LEU* 3.8 15.3 - - + -
307C PHE* 3.5 40.4 - - + +
310C PRO* 4.3 0.4 - - + -
311C ALA* 3.7 17.9 - - + +
317C ARG* 1.3 76.1 - - - +
319C ALA* 1.3 59.9 + - - +
394C PHE* 4.5 9.6 - - + -
395C GLY 3.3 6.1 - - - +
396C ALA* 4.2 12.1 - - + -
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C LEU* 4.5 9.6 - - + -
293C THR 3.7 3.8 - - - +
294C ASP* 4.7 0.4 - - - +
295C VAL* 4.6 2.0 - - - -
317C ARG* 3.8 20.1 - - - +
318C VAL* 1.3 73.4 - - - +
320C ALA* 1.3 59.7 + - - +
393C PHE 3.5 0.9 - - - +
394C PHE* 3.2 6.6 - - - +
395C GLY 2.7 38.9 + - - +
402C VAL* 3.3 29.4 - - + -
406C MET* 4.4 9.7 - - + +
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C GLU 4.0 0.5 - - - +
292C LEU* 3.1 6.7 - - - -
293C THR* 2.7 44.6 + - - +
295C VAL* 4.0 8.5 - - + -
318C VAL 4.1 0.4 + - - -
319C ALA* 1.3 74.7 - - - +
321C LEU* 1.3 60.1 + - - +
322C ARG 4.1 0.6 + - - -
380C ILE* 4.7 0.2 - - + -
384C THR* 3.8 24.2 - - + -
392C ILE* 3.9 5.2 - - + -
393C PHE 3.2 5.2 - - - -
394C PHE* 3.8 22.0 - - + -
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C MET* 4.0 29.4 - - + -
291C GLU 4.1 9.4 - - - +
292C LEU* 4.0 9.0 - - + -
320C ALA* 1.3 73.4 - - - +
322C ARG* 1.3 63.8 + - - +
323C VAL* 3.7 9.3 + - + +
391C MET 3.3 4.3 - - - +
392C ILE* 3.4 2.8 - - - -
393C PHE* 2.7 43.5 + - + +
406C MET* 3.7 17.9 - - + +
409C LEU* 3.4 33.4 - - + +
410C ARG* 4.0 31.0 - - + +
413C VAL* 5.1 4.0 - - + -
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Residues in contact with ARG 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C MET* 3.6 24.1 - - - +
291C GLU 4.1 7.7 + - - +
320C ALA 4.1 1.2 - - - -
321C LEU* 1.3 73.6 - - - +
323C VAL* 1.3 61.1 + - - +
324C PRO* 3.6 23.0 - - - +
384C THR* 3.4 30.2 + - - +
385C ALA* 3.7 14.6 + - - +
386C ALA* 4.4 1.1 - - - -
387C GLN* 3.1 19.0 - - - +
390C ASP* 2.7 39.2 + - - +
391C MET 3.4 3.6 - - - +
392C ILE* 4.0 22.0 - - + -
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Residues in contact with VAL 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C MET* 3.8 12.6 - - - -
321C LEU* 4.0 9.6 - - + +
322C ARG* 1.3 74.6 - - - +
324C PRO* 1.3 67.5 - - + +
325C GLY 3.4 0.2 + - - -
326C GLY* 3.2 27.8 + - - +
329C LEU* 5.9 2.0 - - + -
390C ASP* 3.6 2.5 - - - +
391C MET* 2.8 40.3 + - + +
393C PHE* 3.6 33.0 - - + -
413C VAL* 4.0 11.9 - - + -
417C LEU* 4.2 13.5 - - + -
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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