Contacts of the strand formed by residues 314 - 318 (chain A) in PDB entry 2DOU
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 TYR 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLY* 4.0 15.7 - - - -
168A ASN 4.1 0.7 - - - -
169A ASN* 3.1 48.6 + - + -
170A PRO 3.8 17.3 - - - +
171A THR 4.8 0.3 - - - +
172A GLY* 4.3 6.8 - - - +
200A TYR* 3.9 15.9 + + - -
205A TYR* 4.6 1.0 + - - -
311A ALA 4.0 5.7 - - - +
312A THR* 2.8 37.7 + - - +
313A MET* 1.3 106.5 - - + +
315A LEU* 1.3 70.5 + - - +
316A TRP 4.4 0.2 + - - -
354A ARG* 3.6 37.5 - - + -
355A ILE 3.3 3.6 - - - -
356A ALA* 4.5 2.5 - - - -
357A LEU* 4.6 0.9 - - - -
501A EPE 3.5 21.0 + - - +
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Residues in contact with LEU 315 (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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170A PRO 4.7 0.7 - - - -
205A TYR* 5.1 0.2 - - - +
293A ALA* 3.9 37.2 - - + +
296A MET* 4.2 21.8 - - + -
297A ALA* 4.3 6.1 - - - +
300A LEU* 4.5 8.7 - - + -
306A LEU* 4.1 16.2 - - + -
307A LEU 5.7 1.1 - - - +
309A PRO* 4.2 19.5 - - + -
314A TYR* 1.3 83.3 - - - +
316A TRP* 1.3 60.6 + - - +
317A GLY 3.9 0.7 - - - -
353A VAL 3.6 1.4 - - - +
354A ARG* 3.3 5.7 - - - +
355A ILE* 2.8 47.5 + - + +
357A LEU* 3.8 21.8 - - + -
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Residues in contact with TRP 316 (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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119A VAL* 3.9 19.5 - - + -
140A LEU* 5.3 3.8 - - - +
170A PRO* 3.3 40.4 - - + +
171A THR* 3.5 42.2 + - + +
305A SER 4.2 1.9 - - - +
306A LEU* 3.7 8.8 - - - +
307A LEU* 4.0 31.4 + - + +
315A LEU* 1.3 71.9 - - - +
317A GLY* 1.3 59.5 + - - +
318A ARG 4.1 0.7 + - - -
342A GLY* 3.6 32.3 - - - -
345A PHE* 3.8 9.4 - + - -
348A GLY 4.7 0.2 - - - -
349A GLY* 4.1 8.1 - - - -
352A PHE* 3.2 42.4 - + + -
353A VAL 3.7 8.3 - - - -
354A ARG* 3.7 18.8 - - + -
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Residues in contact with GLY 317 (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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304A LEU* 4.2 14.3 - - - +
305A SER 3.7 3.8 - - - -
306A LEU* 3.5 20.6 - - - +
315A LEU 3.9 0.8 - - - -
316A TRP* 1.3 74.4 - - - +
318A ARG* 1.3 61.8 + - - -
319A LEU 3.7 0.7 + - - -
352A PHE* 3.4 7.5 - - - -
353A VAL* 3.1 38.8 + - - +
355A ILE* 5.7 0.6 - - - +
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Residues in contact with ARG 318 (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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142A GLU* 5.6 7.7 + - - +
303A VAL 4.6 0.2 - - - +
304A LEU* 3.7 6.4 - - - -
305A SER* 3.1 45.9 + - - +
307A LEU* 6.1 2.2 - - - +
316A TRP 4.1 0.4 + - - -
317A GLY* 1.3 71.5 - - - -
319A LEU* 1.3 73.3 + - - +
351A GLY 3.7 7.9 - - - +
352A PHE* 3.5 45.4 - - + -
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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