Contacts of the strand formed by residues 335 - 348 (chain A) in PDB entry 2VDY
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 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLY 3.3 12.1 - - - -
185A TRP* 3.2 21.5 + - - -
331A LEU* 3.9 1.2 - - - -
332A ASN* 2.7 43.2 + - - +
334A GLU* 1.3 77.2 - - - +
336A THR* 1.3 64.9 + - - -
337A GLU* 5.8 0.4 - - - -
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Residues in contact with THR 336 (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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181A PHE* 4.0 6.8 - - + +
182A LYS* 3.5 0.3 - - - -
183A GLY 2.9 33.2 + - - +
185A TRP* 3.4 4.5 - - - -
235A TYR* 2.8 39.0 + - + +
329A LEU* 3.7 21.8 - - + -
330A GLN 3.4 11.2 - - - +
331A LEU* 3.3 17.2 - - + +
335A GLY* 1.3 73.4 - - - -
337A GLU* 1.3 74.6 + - - +
338A ALA* 4.1 2.5 - - + +
365A ILE* 4.4 9.4 - - + -
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Residues in contact with GLU 337 (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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159A LYS* 3.2 36.3 + - - +
180A PHE* 5.6 4.7 - - + -
181A PHE 3.4 5.2 - - - +
182A LYS* 3.9 33.3 - - + +
328A VAL* 4.0 1.0 - - - +
329A LEU* 3.7 1.7 - - - -
330A GLN* 2.8 56.2 + - + +
332A ASN* 5.2 11.2 + - - +
335A GLY 5.8 0.4 - - - -
336A THR* 1.3 79.0 - - - +
338A ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 338 (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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42A PHE* 3.7 22.0 - - + -
159A LYS* 5.8 0.7 - - - -
180A PHE* 4.3 2.6 - - - -
181A PHE* 2.7 48.0 + - + +
328A VAL* 3.4 4.9 - - - +
329A LEU* 4.4 6.7 - - + -
336A THR* 4.1 3.7 - - + -
337A GLU* 1.3 75.0 - - - +
339A ALA* 1.3 59.6 + - - +
365A ILE* 5.0 0.7 - - + -
375A PHE* 3.6 30.2 - - + -
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Residues in contact with ALA 339 (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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156A THR* 4.4 2.0 - - - -
159A LYS* 3.6 33.0 - - + -
160A ILE* 3.9 10.1 - - + -
179A ILE 3.2 12.1 - - - +
180A PHE* 4.3 7.6 - - + -
327A ALA* 3.2 5.9 - - - +
328A VAL* 2.9 36.6 + - + +
338A ALA* 1.3 77.5 - - - +
340A GLY* 1.3 58.3 + - - +
375A PHE* 4.1 8.1 - - - -
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Residues in contact with GLY 340 (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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44A SER* 4.8 1.8 - - - -
47A SER* 4.8 0.9 - - - -
156A THR* 4.3 1.6 - - - +
160A ILE* 4.0 4.0 - - - +
178A TYR* 3.3 3.3 - - - +
179A ILE* 2.7 50.4 + - - +
325A HIS* 4.3 7.6 - - - -
326A LYS 3.3 9.4 - - - -
327A ALA* 4.0 6.3 - - - -
339A ALA* 1.3 75.5 - - - +
341A ALA* 1.3 62.1 + - - +
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Residues in contact with ALA 341 (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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47A SER* 4.7 0.4 - - - -
152A VAL* 3.8 29.2 - - + -
160A ILE* 3.9 15.3 - - + -
163A LEU* 3.9 14.6 - - + +
176A VAL* 5.7 0.2 - - + -
177A ASN 3.2 10.8 - - - +
178A TYR* 4.6 1.6 - - - -
325A HIS* 3.1 8.4 + - - -
326A LYS* 2.8 34.8 + - - +
340A GLY* 1.3 76.1 - - - +
342A MET* 1.3 60.0 + - - +
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Residues in contact with MET 342 (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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47A SER* 4.3 10.0 + - - +
48A ILE* 3.8 34.5 - - + +
51A ALA* 3.8 26.0 - - + -
52A LEU* 4.9 10.8 - - + -
163A LEU* 4.6 2.2 - - - +
175A LEU* 5.6 1.6 - - + -
176A VAL* 3.4 7.8 - - - +
177A ASN* 2.8 30.0 + - + +
290A LEU* 4.0 13.2 - - - -
323A VAL* 3.7 22.0 - - + -
324A VAL 3.4 12.3 - - - +
325A HIS* 3.5 22.7 - - + +
341A ALA* 1.3 71.7 - - - +
343A PHE* 1.3 75.7 + - - +
344A LEU* 4.8 7.2 - - + +
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Residues in contact with PHE 343 (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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163A LEU* 3.5 50.7 - - + -
164A PHE* 3.5 32.8 - + + -
168A ASP* 3.5 21.8 - - - -
174A VAL* 4.3 3.8 - - + -
175A LEU 3.2 9.2 - - - +
176A VAL* 4.4 2.5 - - + -
322A LYS* 4.7 4.7 - - + -
323A VAL* 3.5 5.4 - - - +
324A VAL* 2.9 69.5 + - + -
342A MET* 1.3 80.1 - - - +
344A LEU* 1.3 62.3 + - - +
345A GLU* 3.7 28.7 - - + -
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Residues in contact with LEU 344 (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 ALA 6.1 0.4 - - - +
52A LEU* 4.4 10.1 - - + -
55A LEU* 3.6 48.0 - - + -
173A LEU* 3.8 3.2 - - + +
174A VAL* 3.3 5.4 - - - -
175A LEU* 2.8 54.7 + - + -
302A LEU* 4.9 1.3 - - + -
309A PHE* 4.7 1.6 - - + -
320A SER* 3.9 19.5 - - - +
322A LYS 3.5 2.7 - - - -
323A VAL* 3.8 21.8 - - + +
342A MET* 4.8 6.1 - - + -
343A PHE* 1.3 74.2 - - - +
345A GLU* 1.3 73.3 + - - +
346A ALA* 4.4 9.9 - - + +
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Residues in contact with GLU 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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141A TRP* 3.3 10.4 - - - -
164A PHE* 3.3 26.0 - - + -
168A ASP 3.8 8.7 + - - -
169A SER* 2.7 33.6 + - - +
171A ALA* 3.6 8.7 - - + +
173A LEU 3.6 2.9 - - - -
174A VAL* 4.1 7.9 - - + -
320A SER* 3.4 7.1 + - - -
321A SER* 2.8 39.6 + - - +
322A LYS* 2.9 29.6 + - - +
343A PHE* 3.7 19.8 - - + -
344A LEU* 1.3 73.5 - - - +
346A ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 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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171A ALA* 3.4 4.0 - - - +
172A ILE* 3.3 27.1 + - - +
173A LEU* 2.9 36.8 + - + +
309A PHE* 4.6 5.6 - - + -
318A LEU* 4.0 17.0 - - + -
319A LYS 3.2 13.0 - - - +
344A LEU* 4.0 8.0 + - + -
345A GLU* 1.3 74.8 - - - +
347A ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 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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170A PRO 3.7 22.9 - - - +
171A ALA* 3.9 9.4 - - + -
172A ILE* 3.8 6.1 - - - -
318A LEU* 3.5 3.8 - - - -
319A LYS* 2.9 56.8 + - - +
321A SER* 3.8 27.6 - - - +
346A ALA* 1.3 79.3 - - - +
348A PRO* 1.4 84.8 - - + +
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Residues in contact with PRO 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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138A PHE* 6.5 0.4 - - + -
172A ILE* 3.6 23.5 - - + -
316A ALA* 5.2 9.0 - - + -
317A GLN 3.6 7.9 - - - +
318A LEU* 4.3 5.4 - - + -
319A LYS* 4.5 0.7 - - - +
347A ILE* 1.4 101.4 - - + +
349A ARG* 1.3 68.1 + - - +
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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