Contacts of the strand formed by residues 329 - 336 (chain A) in PDB entry 4Q44
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 VAL 329 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A GLU* 3.4 5.8 - - - +
252A ASP 3.1 15.9 + - - +
253A ILE* 3.2 42.3 + - + +
290A LEU* 4.2 9.6 - - + -
291A LYS 3.4 6.1 - - - +
292A PHE* 3.9 22.2 - - + -
320A TRP* 3.6 23.6 - - + -
324A ARG* 4.2 9.4 - - - -
328A GLY* 1.3 77.7 - - - +
330A ARG* 1.3 60.7 + - - +
331A LEU 3.2 30.5 - - - +
332A VAL* 4.1 3.4 - - + -
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Residues in contact with ARG 330 (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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38A ARG* 3.0 35.3 - - - +
248A THR* 3.2 21.9 + - - +
249A MET* 2.9 32.0 + - - +
251A GLU* 3.4 26.3 + - - +
253A ILE* 5.9 0.4 - - - -
291A LYS* 2.9 30.2 + - + +
292A PHE 3.4 20.6 - - - +
293A ASP* 4.9 3.2 + - - +
295A PHE* 3.6 26.9 - - - +
328A GLY 4.1 1.4 + - - -
329A VAL* 1.3 74.1 - - - +
331A LEU* 1.3 61.9 + - + +
332A VAL* 5.9 0.2 - - - -
839B T 3.1 43.6 + - - +
840B A 3.0 23.6 + - - -
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 4.2 19.5 - - + +
247A ARG 3.1 12.6 - - - +
248A THR* 3.2 21.8 - - - +
289A LYS* 3.5 38.8 - - + +
290A LEU* 3.7 2.3 - - - -
291A LYS* 3.2 53.0 + - + +
297A GLN* 5.8 0.2 - - - +
329A VAL* 3.2 11.1 - - - +
330A ARG* 1.3 84.9 - - + +
332A VAL* 1.3 71.3 + - - +
840B A 5.4 1.3 - - + -
841B RDG 3.2 13.7 - - - +
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Residues in contact with VAL 332 (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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246A GLU* 3.3 1.2 - - - -
247A ARG 2.9 29.7 + - - +
253A ILE* 3.8 28.3 - - + -
259A CYS* 4.3 11.4 - - - +
262A ILE* 3.8 31.4 - - + -
263A ILE* 4.0 27.4 - - + -
266A LEU* 3.4 10.8 - - + +
288A VAL* 4.9 2.2 - - + -
289A LYS 3.7 6.1 - - - +
290A LEU* 4.4 7.2 - - + -
329A VAL* 4.1 2.9 - - + -
331A LEU* 1.3 82.5 - - - +
333A GLY* 1.3 64.7 + - - +
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Residues in contact with GLY 333 (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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245A VAL 3.6 1.3 - - - -
246A GLU* 3.6 18.4 - - - -
266A LEU* 4.4 0.4 - - - -
288A VAL* 3.2 10.4 - - - +
289A LYS* 2.7 50.5 + - - +
332A VAL* 1.3 77.4 - - - +
334A LEU* 1.3 64.9 + - - -
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Residues in contact with LEU 334 (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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244A GLY* 3.2 3.0 - - - -
245A VAL* 2.9 37.7 + - + +
246A GLU* 5.4 1.7 - - - +
263A ILE* 4.2 21.3 - - + +
266A LEU* 3.8 18.4 - - + +
267A TYR* 3.8 34.5 - - + +
270A LEU* 3.6 23.1 - - + -
287A GLY 3.7 2.9 - - - +
288A VAL* 4.3 11.0 - - + -
312A LEU* 3.8 34.3 - - + -
332A VAL* 5.9 0.2 - - + -
333A GLY* 1.3 80.9 - - - +
335A HIS* 1.3 62.9 + - - +
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Residues in contact with HIS 335 (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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242A SER* 3.3 18.7 + - - -
243A VAL* 3.8 16.4 - - - -
244A GLY* 4.3 4.0 - - - -
270A LEU* 4.4 2.8 - - - +
286A GLN* 3.7 1.0 - - - +
287A GLY 2.9 39.1 + - - +
288A VAL* 5.3 2.9 - - - +
289A LYS* 6.1 3.4 - - + -
301A GLU* 2.4 38.4 + - + +
312A LEU* 4.9 0.3 - - - +
334A LEU* 1.3 78.1 - - - +
336A VAL* 1.3 91.6 + - - +
337A THR* 3.8 8.3 - - + -
843B G 5.7 0.9 - - - -
844B T 5.9 2.4 - - - +
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Residues in contact with VAL 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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242A SER* 3.4 8.1 - - - -
243A VAL* 3.0 42.4 + - + +
270A LEU* 4.3 10.3 - - + -
274A LEU* 4.1 9.6 - - + -
283A ILE* 3.7 25.8 - - + -
285A ARG 3.7 4.9 - - - -
286A GLN* 4.2 8.7 - - + -
307A LEU* 4.0 23.8 - - + -
335A HIS* 1.3 100.3 + - - +
337A THR* 1.3 64.0 + - - +
338A LEU* 3.7 9.9 - - + -
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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