Contacts of the strand formed by residues 344 - 357 (chain A) in PDB entry 3NDF
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 3.4 9.6 - - - -
194A TRP* 3.0 27.2 + - - -
244A TYR* 4.7 0.2 - - - -
340A ILE* 3.8 0.2 - - - -
341A ASP* 3.2 31.0 + - - +
343A LYS* 1.3 81.2 - - - +
345A THR* 1.3 68.3 + - - -
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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* 3.6 2.7 - - - -
191A LYS* 3.5 3.6 - - - +
192A GLY 2.9 34.1 + - - +
194A TRP* 3.3 11.4 - - - -
244A TYR* 2.6 34.1 + - - +
338A LEU* 3.5 23.8 - - + -
339A THR 3.3 13.5 - - - +
340A ILE* 3.8 7.4 - - + +
341A ASP* 6.1 0.4 - - - -
344A GLY* 1.3 77.9 + - - -
346A GLU* 1.3 65.6 + - - +
374B MET* 3.6 17.3 - - + -
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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 GLN 5.1 2.6 - - - +
168A LYS* 3.9 21.9 - - + +
189A PHE* 4.4 16.8 - - + -
190A PHE 3.4 11.4 - - - +
191A LYS* 4.6 21.2 + - + +
337A VAL* 3.9 1.7 - - + +
338A LEU* 3.5 1.0 - - - +
339A THR* 2.7 54.5 + - + +
345A THR* 1.3 75.4 - - - +
347A ALA* 1.3 65.7 + - - +
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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* 4.0 12.1 - - + -
189A PHE* 3.7 1.6 - - - -
190A PHE* 2.8 42.7 + - + +
337A VAL* 3.1 10.8 - - - +
338A LEU* 4.3 2.0 - - + -
346A GLU* 1.3 78.8 - - - +
348A ALA* 1.3 60.7 + - - +
374B MET* 4.2 11.0 - - + -
384B PHE* 3.5 32.7 - - + -
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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 9.0 - - - -
168A LYS* 3.8 14.1 - - + -
169A ILE* 3.5 22.2 - - + -
188A ILE 3.2 9.6 - - - +
189A PHE* 4.6 4.0 - - + -
336A ALA* 3.0 6.1 - - - +
337A VAL* 2.7 47.9 + - + +
347A ALA* 1.3 77.1 - - - +
349A GLY* 1.3 58.2 + - - +
384B PHE* 4.0 6.5 - - - -
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Residues in contact with GLY 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* 4.5 9.0 - - - -
56A SER* 4.4 5.4 - - - -
165A THR* 4.5 0.2 - - - +
169A ILE* 3.8 2.0 - - - +
187A TYR* 2.9 4.4 - - - +
188A ILE 2.6 39.5 + - - +
334A HIS* 4.8 0.4 - - - -
335A LYS 3.4 7.6 - - - -
336A ALA* 4.1 7.0 - - - -
348A ALA* 1.3 75.1 - - - +
350A ALA* 1.3 62.1 + - - +
384B PHE* 4.0 9.9 - - - -
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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* 4.4 1.6 + - - -
161A VAL* 4.1 14.4 - - + -
169A ILE* 3.8 17.9 - - + -
172A LEU* 4.0 22.8 - - + +
186A ASN 3.0 10.8 - - - +
187A TYR* 4.2 4.3 - - + -
333A VAL 3.9 0.2 - - - +
334A HIS* 3.5 6.9 + - - -
335A LYS 2.9 31.8 + - - +
349A GLY* 1.3 77.0 - - - +
351A ASP* 1.3 64.7 + - - +
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Residues in contact with ASP 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* 2.4 44.3 + - - -
57A ILE* 3.1 19.6 + - - +
60A ALA* 4.2 12.1 - - + -
61A PHE* 5.5 1.1 - - - -
172A LEU* 4.3 2.2 - - - -
184A LEU 4.0 1.6 - - - -
185A VAL* 3.1 13.0 - - - +
186A ASN* 2.6 41.2 + - + +
299A LEU* 4.4 3.5 - - - +
333A VAL 3.3 3.9 - - - +
334A HIS* 2.9 29.2 + - - +
350A ALA* 1.3 72.3 - - - +
352A ASP* 1.3 61.2 + - - +
353A ASP* 4.4 7.7 - - - +
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Residues in contact with ASP 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* 4.9 0.9 - - - +
172A LEU* 3.9 18.7 - - + +
173A VAL* 3.5 20.9 - - - +
183A ALA* 4.0 7.1 - - - +
184A LEU 3.6 1.3 - - - -
185A VAL* 4.0 14.1 - - + +
331A LYS 3.7 3.5 - - - +
333A VAL* 2.7 54.8 + - + +
351A ASP* 1.3 74.0 - - - +
353A ASP* 1.3 61.7 + - - +
354A GLU* 2.5 39.0 + - - +
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Residues in contact with ASP 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* 3.5 28.4 - - - +
61A PHE* 3.6 25.4 - - - -
64A LEU* 5.8 3.4 - - + +
182A PHE* 4.0 2.6 - - - +
183A ALA* 3.4 1.2 - - - -
184A LEU* 2.7 53.3 + - + +
299A LEU* 6.1 0.3 - - - +
329A LEU* 4.0 20.2 - - + -
331A LYS 3.4 3.6 - - - -
332A ALA* 3.5 15.8 - - - +
333A VAL 4.0 2.8 + - - +
351A ASP* 4.4 4.5 - - - +
352A ASP* 1.3 82.0 + - - +
354A GLU* 1.3 62.3 + - - +
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Residues in contact with GLU 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 VAL* 4.4 5.4 - - - +
175A GLU 4.9 3.7 - - - +
176A LEU* 3.8 29.3 - - + +
177A ASP* 5.0 5.9 + - - +
180A THR* 4.4 11.0 + - + +
182A PHE 3.6 4.9 - - - +
183A ALA* 4.4 6.3 - - + -
329A LEU* 3.2 9.0 - - - +
330A SER* 3.0 32.6 + - - +
331A LYS* 3.0 41.3 + - + +
333A VAL* 5.2 0.2 - - - +
352A ASP* 2.5 39.7 - - - +
353A ASP* 1.3 73.2 - - - +
355A ALA* 1.3 61.0 + - - +
356A ILE* 5.7 1.1 - - + -
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Residues in contact with ALA 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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180A THR* 3.6 2.3 - - - -
181A VAL* 2.8 32.1 + - - -
182A PHE* 2.8 53.3 + - + -
318A LEU* 4.8 1.1 - - + -
327A LEU* 4.8 7.9 - - + -
328A LYS 3.1 12.6 - - - +
329A LEU* 4.2 4.5 - - + -
353A ASP 4.2 0.2 + - - -
354A GLU* 1.3 72.7 - - - +
356A ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 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* 4.3 20.6 - - + +
179A ASP* 4.5 2.0 - - + +
180A THR* 4.1 18.6 - - + +
181A VAL* 4.5 2.7 - - - +
327A LEU* 3.4 7.2 - - - -
328A LYS* 2.6 58.1 + - + +
330A SER* 3.4 33.4 - - - +
354A GLU* 5.3 1.6 - - + -
355A ALA* 1.3 80.3 - - - +
357A PRO* 1.3 82.7 - - + +
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Residues in contact with PRO 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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179A ASP* 3.8 28.5 - - + +
181A VAL* 4.2 12.1 - - + -
325A ALA* 6.0 2.9 - - + -
326A PRO 3.7 8.7 - - - +
327A LEU* 4.2 6.7 - - + -
328A LYS* 4.1 3.1 - - - -
356A ILE* 1.3 101.4 - - + +
358A ARG* 1.3 65.7 + - - +
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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