Contacts of the strand formed by residues 324 - 329 (chain A) in PDB entry 1EAG
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 GLU 324 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ALA* 3.8 25.6 - - + +
186A LEU 3.2 19.1 - - - +
187A PRO* 4.5 2.9 - - + -
188A VAL* 3.7 3.0 - - - +
268A LYS* 5.6 3.6 + - - +
317A VAL 3.7 1.0 - - - +
319A ASP* 2.9 39.7 + - + +
322A ASP* 3.9 24.3 - - - +
323A ASN* 1.3 79.3 - - - +
325A ILE* 1.3 64.7 + - - +
326A SER* 5.3 1.3 - - - +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE 3.8 0.5 - - - +
186A LEU* 2.7 37.8 + - - +
188A VAL* 4.0 15.4 - - + +
194A LEU* 4.0 42.0 - - + +
195A ARG 4.7 0.2 - - - -
196A ILE* 4.1 20.4 - - + -
217A LEU* 4.1 18.4 - - + -
316A ILE* 3.8 26.2 - - + -
317A VAL 3.3 3.8 - - - +
318A TYR* 3.9 20.4 - - + -
324A GLU* 1.3 79.2 - - - +
326A SER* 1.3 60.2 + - - +
327A LEU* 4.2 6.3 - - + -
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.8 25.4 - - - +
184A ILE 3.1 7.2 - - - -
185A ALA* 3.3 24.1 + - - +
315A TYR 3.6 0.6 - - - +
316A ILE* 3.6 7.4 - - - +
317A VAL* 2.9 42.3 + - - +
324A GLU* 4.1 2.1 + - - +
325A ILE* 1.3 71.2 - - - +
327A LEU* 1.3 65.3 + - - +
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Residues in contact with LEU 327 (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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182A SER 3.9 1.7 - - - +
183A LEU* 3.3 4.8 - - - -
184A ILE* 2.9 36.0 + - - +
186A LEU* 4.0 18.8 - - + -
196A ILE* 4.1 5.8 - - + -
217A LEU* 3.9 17.7 - - + -
266A PHE* 3.6 39.0 - - + -
270A ALA* 5.0 9.0 - - + +
272A ILE* 4.2 15.7 - - + -
310A PHE* 4.9 2.5 - - + -
314A ALA* 4.7 7.0 - - + -
315A TYR 3.6 3.6 - - - +
316A ILE* 3.8 25.6 - - + -
325A ILE* 4.2 4.5 - - + -
326A SER* 1.3 84.1 - - - +
328A ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 328 (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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179A TYR* 3.3 29.2 - - + -
180A SER 3.9 5.4 - - - +
182A SER 4.0 9.2 - - - +
183A LEU* 3.2 25.8 - - + -
272A ILE* 3.6 6.8 - - - +
314A ALA* 3.6 4.0 - - - -
315A TYR* 2.9 28.3 + - + -
327A LEU* 1.3 72.6 - - - +
329A GLN* 1.3 61.0 + - - +
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Residues in contact with GLN 329 (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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179A TYR* 3.0 4.9 - - - +
180A SER* 2.9 45.0 + - - +
271A LYS 4.2 4.6 + - - +
272A ILE* 3.7 11.2 - - + +
273A SER* 2.9 53.6 + - - -
313A SER* 3.2 21.4 + - - +
328A ALA* 1.3 71.3 - - - +
330A VAL* 1.3 72.6 + - - +
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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