Contacts of the strand formed by residues 319 - 325 (chain A) in PDB entry 1EBF
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 ASN 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLY* 4.1 15.3 - - - +
150A LEU* 4.5 9.4 - - + -
172A ILE* 3.2 13.4 - - - +
173A PHE* 3.3 30.4 + - + +
174A SER* 3.6 1.8 - - - +
175A GLY* 3.5 24.3 + - - +
223A LYS* 4.8 0.2 - - - +
317A SER 3.9 0.2 - - - +
318A ASP* 1.3 76.9 - - - +
320A VAL* 1.3 72.6 + - - +
335A GLN* 3.4 0.8 - - - -
336A GLY 2.8 31.5 + - - +
338A GLY* 3.6 28.6 + - - +
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Residues in contact with VAL 320 (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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150A LEU* 5.7 0.7 - - - -
152A ILE* 6.0 1.3 - - - -
171A GLY* 3.1 4.8 - - - -
172A ILE* 3.0 32.0 + - + +
173A PHE* 4.5 2.9 - - - -
310A PRO* 5.7 0.7 - - + -
311A PHE* 3.7 24.0 - - + -
314A LEU* 3.0 44.6 - - + -
319A ASN* 1.3 88.3 - - - +
321A ILE* 1.3 64.9 + - - +
333A VAL* 3.6 26.0 - - + -
334A ILE 3.1 14.1 - - - +
335A GLN* 3.4 10.3 - - + -
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Residues in contact with ILE 321 (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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152A ILE* 3.7 39.9 - - + -
156A LEU* 5.0 0.7 - - + -
169A ILE* 3.7 29.4 - - + -
170A GLU 3.7 3.8 - - - +
173A PHE* 3.9 21.1 - - + -
227A VAL* 4.6 10.5 - - + -
320A VAL* 1.3 79.8 - - - +
322A SER* 1.3 61.8 + - - +
323A ILE* 3.8 25.6 - - + -
332A VAL 3.4 0.7 - - - +
333A VAL* 3.3 5.7 - - - +
334A ILE* 2.9 47.1 + - + +
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Residues in contact with SER 322 (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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168A LYS 3.9 0.2 - - - +
169A ILE* 3.3 9.9 - - - +
170A GLU* 2.8 52.7 + - - +
309A HIS* 5.7 1.9 + - - -
311A PHE* 4.1 14.3 - - - -
321A ILE* 1.3 72.7 - - - +
323A ILE* 1.3 58.4 + - - +
324A LYS* 4.2 4.1 - - - +
331A PRO* 3.4 24.9 - - - +
332A VAL 3.5 3.8 - - - -
333A VAL* 4.2 7.4 - - - +
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Residues in contact with ILE 323 (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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152A ILE* 4.9 3.1 - - + -
155A PHE* 4.4 21.5 - - + -
156A LEU* 3.8 34.5 - - + -
166A VAL* 4.9 1.3 - - + -
168A LYS 3.8 1.8 - - - -
169A ILE* 4.2 11.7 - - + -
321A ILE* 3.8 35.0 - - + -
322A SER* 1.3 80.0 + - - +
324A LYS* 1.3 63.8 + - - +
325A THR* 3.8 22.6 + - + -
328A TYR* 4.2 2.4 - - - +
331A PRO* 3.5 2.1 - - - +
332A VAL* 2.8 52.6 + - + +
334A ILE* 4.9 2.9 - - + -
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Residues in contact with LYS 324 (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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166A VAL* 3.9 1.7 - - - +
167A GLU* 2.9 27.6 + - + +
168A LYS* 2.8 46.8 + - + +
170A GLU* 5.8 2.5 + - - -
322A SER* 5.1 4.3 - - - +
323A ILE* 1.3 72.7 - - - +
325A THR* 1.3 63.4 + - - +
328A TYR 3.7 4.7 - - - +
329A THR* 4.3 13.2 - - - +
331A PRO* 3.2 40.4 - - + -
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Residues in contact with THR 325 (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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155A PHE* 6.3 1.3 - - + -
156A LEU* 5.9 0.2 - - + -
159A ILE* 4.6 7.6 - - + -
164A ASP* 2.7 35.4 + - - +
165A GLU 3.1 11.4 - - - +
166A VAL* 4.2 12.3 - - + -
167A GLU* 4.0 11.2 - - - +
323A ILE* 3.8 21.5 + - + -
324A LYS* 1.3 80.5 - - - +
326A LYS* 1.3 65.2 + - - +
327A ARG 3.1 0.3 + - - -
328A TYR* 2.9 42.5 + - + +
329A THR* 3.8 5.2 + - - +
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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