Contacts of the strand formed by residues 344 - 357 (chain A) in PDB entry 4CAA
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 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ALA 4.3 9.4 - - - -
194A TRP* 2.9 36.5 - - - -
244A TYR* 4.7 6.5 - - - -
339A ASP 3.1 13.7 - - - +
340A VAL* 3.7 4.3 - - - +
341A PHE 2.7 15.9 + - - -
343A GLU* 1.3 72.4 - - - +
345A ARG* 1.3 66.2 + - - +
346A GLU 3.8 0.2 + - - -
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Residues in contact with ARG 345 (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* 5.1 0.2 - - - +
191A LYS* 3.5 30.5 + - - +
192A ALA 3.7 14.9 + - - +
339A ASP* 3.2 27.4 + - + +
341A PHE* 3.2 49.8 - - + -
343A GLU* 2.7 47.0 + - + +
344A GLY* 1.3 72.3 - - - +
346A GLU* 1.3 98.9 + - - +
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Residues in contact with GLU 346 (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 ARG* 5.7 0.2 - - - +
168A LYS* 3.1 36.1 + - + +
189A PHE* 3.5 18.9 - - + -
190A PHE* 3.5 17.9 - - - +
191A LYS* 3.3 18.9 + - + +
338A LEU* 3.7 1.7 - - - +
339A ASP* 2.8 43.1 + - - +
344A GLY 3.8 0.6 + - - -
345A ARG* 1.3 115.6 + - - +
347A ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 347 (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* 3.3 1.3 - - - +
189A PHE* 4.6 0.3 - - - -
190A PHE* 3.1 33.4 + - + +
337A VAL 3.2 12.6 - - - +
338A LEU* 3.8 20.9 - - + -
346A GLU* 1.3 77.3 - - - +
348A SER* 1.3 67.4 + - - +
374B ILE* 4.4 5.4 - - + -
384B PHE* 3.8 30.1 - - + -
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Residues in contact with SER 348 (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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165A THR* 4.1 19.7 - - - -
168A LYS* 3.1 29.2 - - - +
169A ILE* 4.2 9.6 - - - -
188A ILE 3.2 14.8 - - - -
189A PHE* 3.5 9.9 - - - -
336A ALA* 3.4 0.7 - - - +
337A VAL* 2.8 34.1 + - - +
347A ALA* 1.3 78.9 + - - +
349A ALA* 1.3 61.7 + - - +
384B PHE* 3.7 6.4 - - - -
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Residues in contact with ALA 349 (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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53A SER* 3.5 32.3 - - - -
56A SER* 4.4 0.9 - - - -
165A THR* 4.4 1.6 - - - +
169A ILE* 4.2 4.9 - - - +
187A TYR* 3.4 1.4 - - - +
188A ILE* 2.9 34.2 + - + +
334A HIS* 3.8 6.1 - - + -
335A LYS 3.2 13.2 - - - +
336A ALA* 3.8 11.0 - - + +
348A SER* 1.3 78.9 - - - +
350A ALA* 1.3 63.7 + - - +
384B PHE* 4.1 2.0 - - + -
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Residues in contact with ALA 350 (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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56A SER* 4.1 2.0 - - - -
161A VAL* 3.6 31.9 - - + -
165A THR* 5.0 0.2 - - + -
169A ILE* 4.3 7.8 - - + +
172A LEU* 3.7 12.5 - - + +
186A ASN 3.4 14.1 - - - +
187A TYR* 3.6 6.3 - - + +
334A HIS* 2.9 15.4 + - - -
335A LYS 2.9 21.0 + - - -
349A ALA* 1.3 78.4 - - - +
351A THR* 1.3 63.8 + - - +
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Residues in contact with THR 351 (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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56A SER* 3.4 17.5 + - - -
57A ILE* 3.8 15.1 - - + +
60A ALA* 4.2 18.4 - - + +
61A LEU* 6.5 0.4 - - + -
172A LEU* 4.3 3.8 - - - -
184A LEU 3.9 0.4 - - - +
185A VAL* 3.1 5.2 - - - +
186A ASN* 2.8 33.7 + - - +
299A LEU* 5.2 0.2 - - + -
332A VAL* 4.2 17.5 - - + -
333A VAL 3.3 16.4 - - - +
334A HIS* 2.5 30.8 + - + +
350A ALA* 1.3 71.2 - - - +
352A ALA* 1.3 65.5 + - - +
353A VAL* 5.2 0.9 - - + -
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Residues in contact with ALA 352 (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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157A ILE* 5.7 0.4 - - + -
172A LEU* 3.8 20.3 - - + +
173A ILE* 3.9 13.9 - - + -
183A VAL* 3.9 15.9 - - + -
184A LEU 3.1 9.0 - - - +
185A VAL* 4.2 4.5 - - + -
331A GLN 4.0 0.3 - - - +
332A VAL* 3.6 3.8 - - - +
333A VAL* 3.3 35.1 + - + +
351A THR* 1.3 78.9 - - - +
353A VAL* 1.3 65.4 + - - +
354A LYS* 3.9 2.3 + - + +
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Residues in contact with VAL 353 (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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60A ALA* 4.7 21.1 - - + +
61A LEU* 4.5 14.4 - - + -
64A LEU* 4.3 19.7 - - + -
183A VAL* 3.4 4.1 - - - -
184A LEU* 2.8 39.2 + - + +
329A VAL* 4.4 11.7 - - + -
331A GLN 3.9 3.6 - - - -
332A VAL* 3.7 26.7 - - + -
351A THR* 5.2 0.7 - - + -
352A ALA* 1.3 75.6 - - - +
354A LYS* 1.3 56.8 + - - +
355A ILE* 3.2 26.3 + - + +
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Residues in contact with LYS 354 (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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173A ILE* 4.0 21.5 - - + +
174A LYS* 4.5 6.7 - - - +
175A ASP* 3.0 36.0 + - - +
176A LEU* 5.0 7.2 - - + -
177A ASP 5.9 1.6 - - - +
180A THR* 5.3 5.8 - - + +
183A VAL* 4.1 23.8 - - + -
330A SER* 2.8 43.5 + - - +
331A GLN* 3.1 51.7 + - + +
333A VAL* 4.1 18.0 - - - +
352A ALA 4.9 2.7 - - - +
353A VAL* 1.3 68.4 - - - +
355A ILE* 1.3 60.0 + - - +
356A THR* 4.7 1.3 - - + -
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Residues in contact with ILE 355 (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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64A LEU* 4.2 22.0 - - + -
180A THR* 3.6 4.0 - - - +
181A MET* 3.1 20.4 + - - -
182A MET* 2.8 39.8 + - + +
183A VAL* 4.7 0.2 - - - +
184A LEU* 4.3 17.3 - - + -
318A LEU* 4.8 3.1 - - + -
321A ILE* 4.5 13.9 - - + -
327A LEU* 3.7 28.0 - - + -
328A ALA 3.5 15.7 - - - +
329A VAL* 4.8 6.5 - - + -
330A SER 4.6 0.2 - - - +
353A VAL* 3.8 15.9 - - + +
354A LYS* 1.3 72.8 - - - +
356A THR* 1.3 71.7 + - - +
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Residues in contact with THR 356 (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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177A ASP* 4.5 14.6 - - + +
179A GLN* 3.9 25.4 + - + -
180A THR* 4.6 11.0 - - + +
181A MET* 4.2 5.2 - - - +
327A LEU* 3.4 4.8 - - - -
328A ALA* 3.0 38.1 + - - +
329A VAL 5.4 0.2 - - - -
330A SER* 3.4 30.9 - - - +
354A LYS* 4.1 2.5 - - + +
355A ILE* 1.3 79.2 - - - +
357A LEU* 1.3 69.4 + - - +
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Residues in contact with LEU 357 (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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124A LEU* 5.6 1.1 - - + -
179A GLN* 3.7 23.9 + - + +
181A MET* 3.2 46.9 - - + +
326A ASN* 3.4 33.0 - - + +
327A LEU* 4.1 0.2 - - + -
328A ALA* 5.1 1.6 + - - +
356A THR* 1.3 87.7 + - - +
358A LEU* 1.3 65.4 + - - +
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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