Contacts of the helix formed by residues 322 - 333 (chain A) in PDB entry 3ECP
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 ARG 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ILE* 3.8 20.8 - - + +
96A GLU 4.7 1.2 + - - +
97A ASP* 3.0 33.9 + - - +
186A VAL* 4.2 13.0 - - + +
187A CYS* 4.1 2.0 - - - +
188A ASP* 3.5 40.6 + - - +
318A ILE 4.4 0.8 + - - -
319A TYR* 2.9 28.1 + - + +
320A THR 3.4 0.4 - - - -
321A HIS* 1.3 72.2 - - - +
323A TRP* 1.3 54.4 + - - +
324A ARG 2.7 17.2 + - - -
325A ILE* 3.2 32.4 + - - +
1C C 2.7 64.5 + - + +
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Residues in contact with TRP 323 (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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320A THR* 3.1 28.5 + - - +
321A HIS* 3.7 17.1 + - - +
322A ARG* 1.3 76.0 - - - +
324A ARG* 1.3 81.3 + - + +
325A ILE 3.2 0.4 - - - -
326A GLU* 2.9 23.6 + - + +
327A GLU* 2.9 47.7 + - + -
367A ARG* 4.8 3.1 - - - -
1C C 4.1 20.4 - - + +
3C G 3.9 37.7 - - + +
4C A 3.4 46.8 + - - -
5C C 4.6 7.2 - - - -
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Residues in contact with ARG 324 (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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95A ILE* 3.9 10.8 - - + -
130A LEU* 3.9 10.6 - - + +
132A LEU* 3.5 22.8 - - + +
136A THR 4.9 0.8 + - - -
137A PHE* 2.4 39.7 + - - +
138A ARG* 4.6 0.8 - - - +
139A THR* 3.0 27.7 + - - -
321A HIS* 3.1 23.5 + - + +
322A ARG 2.7 6.7 + - - -
323A TRP* 1.3 104.2 - - + +
325A ILE* 1.3 55.8 + - - +
327A GLU* 3.2 28.3 + - - +
328A PHE* 3.0 25.3 + - - +
364A LEU* 5.1 1.0 - - - +
367A ARG* 5.8 0.8 - - - +
368A GLU* 3.7 11.4 + - - +
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Residues in contact with ILE 325 (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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95A ILE* 3.8 27.2 - - + +
97A ASP* 3.8 32.1 - - + +
128A SER* 4.2 13.9 - - - +
130A LEU* 3.8 27.3 - - + +
322A ARG* 3.2 25.4 + - - +
324A ARG* 1.3 76.9 - - - +
326A GLU* 1.3 63.9 + - + +
328A PHE* 3.4 20.9 + - + +
329A HIS* 3.0 44.6 + - + +
20B G 5.8 0.2 - - - +
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Residues in contact with GLU 326 (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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323A TRP* 2.9 12.3 + - + +
325A ILE* 1.3 79.6 - - + +
327A GLU* 1.3 61.1 + - - +
329A HIS* 3.1 13.0 + - - +
330A LYS* 2.8 29.8 + - + +
18B C 4.2 1.2 - - - +
19B A 3.7 16.9 + - - +
20B G 3.3 37.0 + - - +
1C C 2.7 39.6 + - - +
3C G 3.3 36.6 + - - +
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Residues in contact with GLU 327 (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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323A TRP* 2.9 43.2 + - + +
324A ARG* 3.2 29.6 + - - +
325A ILE 3.2 0.4 - - - -
326A GLU* 1.3 78.6 - - - +
328A PHE* 1.3 56.7 + - - +
330A LYS* 3.4 8.1 + - - +
331A ALA* 2.8 27.9 + - - +
364A LEU* 3.6 22.3 - - + +
367A ARG* 3.1 28.6 + - - -
368A GLU* 5.1 2.3 - - - +
446A TRP* 3.4 20.7 + - - +
4C A 5.1 0.7 - - - +
5C C 4.7 0.9 + - - -
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Residues in contact with PHE 328 (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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128A SER* 3.9 5.2 - - - -
130A LEU* 4.2 14.1 - - + -
142A LEU* 3.6 23.1 - - + -
145A GLN* 3.6 23.1 - - - -
324A ARG 3.0 13.0 + - - +
325A ILE* 3.4 16.8 - - + +
327A GLU* 1.3 73.9 - - - +
329A HIS* 1.3 75.2 + + - +
331A ALA* 2.8 3.8 + - - +
332A TRP* 2.7 48.6 + + + +
357A SER* 3.4 24.0 - - - -
360A ALA* 3.9 12.8 - - + -
361A VAL* 3.7 20.9 - - + -
364A LEU* 3.9 18.9 - - + +
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Residues in contact with HIS 329 (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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97A ASP* 4.1 13.3 + - + -
98A THR 3.7 13.2 - - - -
99A THR* 3.5 40.3 + - + +
126A VAL 5.0 0.4 + - - -
128A SER* 4.4 4.9 + - - -
325A ILE* 3.0 40.6 + - + +
326A GLU* 3.1 6.6 + - - +
328A PHE* 1.3 97.1 - + - +
330A LYS* 1.3 56.5 + - - +
332A TRP* 3.3 6.4 + + - +
333A LYS* 2.9 35.5 + - + +
19B A 3.9 7.6 - - - +
20B G 2.4 33.2 + - - +
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Residues in contact with LYS 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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326A GLU* 2.8 20.8 + - + +
327A GLU* 3.6 8.1 - - - +
329A HIS* 1.3 68.8 - - - +
331A ALA* 1.3 65.8 + - - +
333A LYS 3.3 0.2 + - - -
334A THR* 3.2 29.3 + - - +
335A GLY 3.1 18.4 + - - -
446A TRP* 3.9 18.2 - - + +
17B T 3.9 8.9 + - - -
18B C 2.8 52.8 + - - +
19B A 3.4 16.7 - - - +
3C G 4.5 8.6 - - - +
4C A 4.6 5.8 - - - -
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Residues in contact with ALA 331 (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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327A GLU 2.8 14.2 + - - +
328A PHE 2.8 12.4 + - - +
330A LYS* 1.3 71.6 - - - +
332A TRP* 1.3 57.3 + - - +
335A GLY* 3.5 0.9 - - - -
336A ALA* 2.7 32.1 + - - +
360A ALA* 3.6 29.5 - - + +
363A LEU* 4.0 5.9 - - + +
364A LEU* 4.0 15.7 - - + -
446A TRP* 3.6 18.3 - - + -
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Residues in contact with TRP 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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99A THR* 4.3 18.2 - - + -
101A LEU* 3.7 26.5 - - + -
126A VAL* 3.8 21.5 - - + -
128A SER* 4.7 0.7 - - - -
145A GLN* 3.5 27.1 - - - -
147A TRP* 3.7 10.8 - + - -
328A PHE* 2.7 36.4 + + + +
329A HIS* 3.5 8.3 - + - +
331A ALA* 1.3 72.8 - - - +
333A LYS* 1.3 65.0 + - + +
336A ALA* 3.7 2.0 + - - +
337A GLY 3.2 5.9 + - - -
338A ALA* 3.1 24.5 + - + +
353A VAL* 3.2 46.2 + - + +
356A LEU* 3.7 6.9 - - + +
357A SER* 3.2 30.4 - - - +
360A ALA* 3.5 9.3 - - + +
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Residues in contact with LYS 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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99A THR* 2.8 32.4 + - + +
100A SER* 2.9 29.0 + - - +
101A LEU* 4.6 11.4 - - + -
329A HIS* 2.9 28.0 + - + +
330A LYS 3.3 0.4 + - - -
332A TRP* 1.3 72.0 - - + +
334A THR* 1.3 62.3 + - - +
337A GLY* 2.8 34.1 + - - -
338A ALA* 4.2 6.1 - - + +
339A GLU* 3.6 35.9 - - + +
340A ARG* 3.9 1.7 + - - +
19B A 2.9 42.6 + - - +
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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