Contacts of the strand formed by residues 344 - 356 (chain A) in PDB entry 1HLE
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 GLY 3.3 12.6 - - - -
193A ASN* 5.2 0.2 - - - -
194A TRP* 3.2 23.0 + - - +
244A TYR* 4.5 0.7 - - - -
339A ASP 4.0 0.3 - - - +
340A LEU* 3.7 0.3 - - - -
341A ASN* 3.1 32.4 + - - +
343A GLU* 1.3 81.8 - - - +
345A THR* 1.3 65.7 + - - -
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Residues in contact with THR 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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190A PHE* 3.9 4.0 - - + +
191A LYS* 3.4 4.6 - - - +
192A GLY 3.1 30.9 + - - +
194A TRP* 3.5 11.3 - - - -
244A TYR* 2.8 32.9 + - - +
250A MET* 4.4 3.6 - - + -
338A VAL* 3.7 28.3 - - + -
339A ASP 3.3 7.0 - - - +
340A LEU* 3.8 7.1 - - - +
344A GLY* 1.3 78.2 + - - -
346A GLU* 1.3 65.6 - - - +
347A ALA* 4.1 1.1 - - + -
374B ILE* 4.0 15.5 - - + -
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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 GLU* 4.5 1.0 - - - +
168A LYS* 2.9 40.0 + - + -
189A TYR* 2.7 37.6 + - + +
190A PHE 3.3 5.2 - - - +
191A LYS* 4.0 23.2 - - + +
337A PHE* 3.8 10.3 - - + -
338A VAL* 3.4 2.1 - - - +
339A ASP* 2.8 49.0 + - + +
345A THR* 1.3 73.9 - - - +
347A ALA* 1.3 60.4 + - - +
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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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51A PHE* 4.4 0.2 - - + -
189A TYR* 3.6 3.5 - - - -
190A PHE* 2.8 36.5 + - + +
337A PHE* 3.2 10.3 - - - +
338A VAL* 4.2 13.2 - - + -
345A THR* 4.1 2.2 - - + -
346A GLU* 1.3 73.8 - - - +
348A ALA* 1.3 62.0 + - - +
374B ILE* 4.3 10.5 - - + -
384B PHE* 3.7 35.3 - - + -
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Residues in contact with ALA 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* 3.9 24.7 - - + -
168A LYS* 3.9 21.3 - - + -
169A ILE* 4.2 4.9 - - + -
188A ILE 3.4 11.4 - - - +
189A TYR* 3.9 7.9 - - + -
336A SER* 3.4 1.4 - - - -
337A PHE* 2.8 33.3 + - + +
347A ALA* 1.3 77.1 - - - +
349A ALA* 1.3 63.4 + - - +
384B PHE* 3.8 6.0 - - - -
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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* 3.4 33.0 - - - -
56A SER* 4.5 0.2 - - - -
165A THR* 4.0 3.6 - - - +
169A ILE* 4.2 5.4 - - - -
187A ALA* 3.5 1.2 - - - -
188A ILE* 2.9 35.7 + - + +
334A HIS* 3.8 9.4 - - + +
335A LYS 3.2 14.1 - - - +
336A SER* 4.1 4.7 - - - +
348A ALA* 1.3 77.8 - - - +
350A ALA* 1.3 63.2 + - - +
384B PHE* 4.0 2.2 - - + -
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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 1.6 - - - -
161A VAL* 3.6 31.9 - - + -
169A ILE* 4.5 4.5 - - + +
172A LEU* 3.7 19.3 - - + +
186A ASN 3.1 14.6 - - - +
187A ALA* 4.2 2.9 - - + -
334A HIS* 3.3 5.1 + - - -
335A LYS 3.0 30.4 + - - -
349A ALA* 1.3 76.8 - - - +
351A THR* 1.3 62.3 + - - +
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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* 2.8 24.7 + - - -
57A ILE* 3.7 14.2 + - + -
60A ALA* 3.8 25.7 - - + +
172A LEU* 4.2 2.2 - - - -
184A LEU 3.8 1.1 - - - +
185A VAL* 3.4 5.2 - - - +
186A ASN* 2.9 31.9 + - - +
332A ILE* 3.8 22.0 - - + -
333A ILE 3.2 12.1 - - - +
334A HIS* 2.9 17.7 + - + +
350A ALA* 1.3 70.5 - - - +
352A ALA* 1.3 61.9 + - - +
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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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172A LEU* 3.8 16.3 - - + +
173A LEU* 3.7 30.5 - - + -
183A VAL* 4.2 13.7 - - + -
184A LEU 3.4 7.0 - - - +
185A VAL* 4.7 3.1 - - + -
331A LYS 3.8 1.0 - - - +
332A ILE* 3.3 5.0 - - - +
333A ILE* 3.0 33.6 + - + +
351A THR* 1.3 77.2 - - - +
353A GLY* 1.3 59.5 + - - +
354A THR* 4.0 1.7 - - + +
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Residues in contact with GLY 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* 5.4 2.8 - - - +
64A ILE* 4.4 14.8 - - - -
182A LEU 3.9 0.9 - - - +
183A VAL* 3.3 5.0 - - - +
184A LEU* 3.0 37.7 + - - +
329A VAL* 4.8 0.9 - - - -
331A LYS 3.4 7.0 - - - -
332A ILE* 4.0 13.0 - - - -
352A ALA* 1.3 72.4 - - - +
354A THR* 1.3 61.4 + - - -
355A ILE* 4.0 6.0 + - - -
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Residues in contact with THR 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 LEU* 4.4 20.9 - - + -
177A MET* 3.9 22.9 + - + +
178A VAL* 4.5 3.1 - - + -
180A THR* 5.0 0.7 - - - -
182A LEU 3.9 2.7 - - - -
183A VAL* 4.0 21.1 - - + -
329A VAL* 3.3 6.1 - - - +
330A SER* 2.9 45.5 + - - -
331A LYS* 2.9 23.5 + - + +
333A ILE* 6.4 1.1 - - + -
352A ALA* 5.1 0.9 - - + -
353A GLY* 1.3 75.1 - - - +
355A ILE* 1.3 60.8 + - - +
356A LEU* 4.3 5.6 - - - -
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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 ILE* 4.7 6.1 - - + -
180A THR* 3.7 0.9 - - - +
181A LYS* 2.9 24.1 + - - -
182A LEU* 2.8 33.9 + - + +
184A LEU* 3.7 28.7 - - + -
318A LEU* 3.8 13.2 - - + -
321A MET* 4.7 3.8 - - + -
327A LEU* 3.8 36.1 - - + -
328A PHE 3.3 11.7 - - - +
329A VAL* 3.3 30.3 - - + -
353A GLY 4.3 2.2 - - - +
354A THR* 1.3 74.5 - - - +
356A LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 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 MET 5.1 3.6 - - - +
179A MET* 3.7 34.1 - - + +
180A THR* 3.6 27.1 - - + +
181A LYS 4.5 0.2 - - - +
314A ARG* 5.7 4.7 - - - +
327A LEU* 3.3 9.0 - - - +
328A PHE* 2.8 48.1 + - + +
330A SER* 3.4 34.8 - - - +
354A THR* 4.2 5.2 - - - -
355A ILE* 1.3 86.6 - - - +
357A LEU* 1.3 64.6 + - - +
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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