Contacts of the helix formed by residues 320 - 341 (chain A) in PDB entry 4U6Q
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 SER 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLU* 2.8 31.7 + - - -
318A TRP 3.5 3.0 + - - -
319A TYR* 1.3 87.8 - - - +
321A GLU* 1.3 64.9 + - - +
322A GLN* 3.6 5.9 + - - +
323A ALA* 2.9 17.3 + - - +
324A SER* 2.9 24.3 + - - -
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Residues in contact with GLU 321 (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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319A TYR* 3.9 21.6 - - - +
320A SER* 1.3 73.2 - - - +
322A GLN* 1.3 66.7 + - + +
324A SER* 3.5 2.2 + - - -
325A ILE* 3.2 44.1 + - + +
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Residues in contact with GLN 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 5.2 2.2 - - - +
320A SER* 3.2 6.4 + - - +
321A GLU* 1.3 80.3 - - + +
323A ALA* 1.3 58.0 + - - +
325A ILE* 4.0 5.7 - - - +
326A GLU* 3.0 38.3 + - - +
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA* 3.7 13.7 - - - +
124A SER* 3.3 23.8 - - - +
127A GLU* 3.6 13.6 + - - +
318A TRP 3.9 5.4 - - - +
320A SER* 2.9 22.6 + - - +
322A GLN* 1.3 74.6 - - - +
324A SER* 1.3 67.3 + - - +
326A GLU* 3.0 8.4 + - - +
327A MET* 2.9 28.5 + - - +
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Residues in contact with SER 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A TRP* 3.9 30.7 - - - -
319A TYR* 4.1 12.3 - - - -
320A SER 2.9 17.2 + - - -
321A GLU* 3.8 4.9 - - - -
323A ALA* 1.3 77.2 - - - +
325A ILE* 1.3 63.8 + - - +
327A MET* 3.4 4.7 - - - +
328A ARG* 3.1 44.4 + - - +
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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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40A VAL* 3.7 25.1 - - + +
321A GLU* 3.2 40.9 + - + +
322A GLN* 4.0 5.6 - - - +
324A SER* 1.3 78.4 - - - +
326A GLU* 1.3 63.5 + - - +
328A ARG* 3.4 4.4 + - - +
329A GLU* 3.0 49.7 + - - +
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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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122A ALA 5.3 0.2 - - - +
123A ALA* 3.9 26.4 - - + +
322A GLN* 3.0 26.9 + - - +
323A ALA* 3.0 6.8 + - - +
325A ILE* 1.3 76.3 - - - +
327A MET* 1.3 58.6 + - - +
329A GLU* 3.2 11.9 + - - +
330A GLU* 3.0 27.8 + - - +
333A ARG* 4.7 4.0 + - - +
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Residues in contact with MET 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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76A TYR* 5.2 0.4 - - - -
98A ILE* 3.6 23.7 - - + +
99A GLY* 4.1 2.0 - - - -
120A VAL* 3.6 26.2 - - + +
123A ALA* 3.5 18.1 - - + +
124A SER* 3.2 26.9 - - - +
318A TRP* 3.6 19.1 - - + -
323A ALA 2.9 12.2 + - - +
324A SER* 3.4 13.2 - - - +
326A GLU* 1.3 73.6 - - - +
328A ARG* 1.3 60.3 + - + +
330A GLU* 3.8 0.2 - - - +
331A ALA* 3.0 28.2 + - - +
402A 3CR 3.3 45.3 - - - +
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Residues in contact with ARG 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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37A ASP* 2.8 45.1 + - - +
39A THR* 4.6 0.8 + - - -
40A VAL* 3.4 36.6 - - + +
41A GLU* 2.8 47.1 + - - +
76A TYR* 3.8 22.8 + - + +
98A ILE* 4.0 14.1 - - + -
324A SER* 3.1 30.8 + - - +
325A ILE* 3.7 3.5 - - - +
326A GLU 3.2 0.4 - - - -
327A MET* 1.3 76.1 - - + +
329A GLU* 1.3 65.3 + - - +
331A ALA* 3.8 3.2 - - - +
332A ALA* 3.1 24.1 + - - +
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Residues in contact with GLU 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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40A VAL* 3.6 16.5 - - + +
44A ILE* 3.5 22.0 - - + +
325A ILE* 3.0 40.7 + - - +
326A GLU* 3.6 12.4 - - - +
328A ARG* 1.3 74.8 - - - +
330A GLU* 1.3 63.0 + - - +
332A ALA 3.6 0.2 + - - -
333A ARG* 3.1 47.0 + - - +
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Residues in contact with GLU 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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119A ASN 5.3 0.2 - - - +
120A VAL* 4.0 26.0 - - + -
121A PRO* 6.0 0.4 - - + -
326A GLU 3.0 16.8 + - - +
327A MET 3.8 4.0 - - - +
329A GLU* 1.3 76.1 - - - +
331A ALA* 1.3 64.8 + - - +
333A ARG* 3.0 29.7 + - - +
334A GLU* 3.0 21.2 + - + +
337A ARG* 2.9 29.0 + - - -
348A LYS* 4.6 4.9 - - - +
349A ASN* 3.9 18.3 - - - +
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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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74A LEU* 3.8 13.7 - - + -
96A VAL* 3.5 25.5 - - + +
98A ILE* 3.9 15.5 - - + -
120A VAL* 4.1 7.0 - - + -
327A MET 3.0 18.6 + - - +
328A ARG 3.8 4.5 - - - +
329A GLU 3.3 0.2 - - - -
330A GLU* 1.3 78.2 - - - +
332A ALA* 1.3 56.4 + - - +
334A GLU* 3.1 5.8 + - - +
335A ILE* 2.9 32.3 + - - +
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Residues in contact with ALA 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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41A GLU* 4.1 15.0 - - + -
44A ILE* 3.7 26.5 - - + -
45A LEU* 3.4 23.4 - - + +
74A LEU* 4.6 2.1 - - - +
328A ARG 3.1 15.3 + - - +
329A GLU 3.9 2.2 - - - +
331A ALA* 1.3 78.6 - - - +
333A ARG* 1.3 57.9 + - - +
335A ILE* 3.1 11.9 + - - +
336A ARG* 2.8 25.5 + - - +
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Residues in contact with ARG 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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44A ILE* 4.0 21.4 - - + +
326A GLU* 4.7 3.8 + - - +
329A GLU* 3.1 46.6 + - - +
330A GLU* 3.0 42.0 + - - +
331A ALA 3.2 0.2 - - - -
332A ALA* 1.3 75.6 - - - +
334A GLU* 1.3 58.1 + - - +
336A ARG* 3.2 6.1 + - - +
337A ARG* 2.8 51.7 + - - +
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Residues in contact with GLU 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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94A ILE* 4.5 2.5 - - + -
96A VAL* 3.9 20.6 - - + -
118A CYS* 3.4 28.9 - - + +
119A ASN 5.7 1.3 - - - +
330A GLU* 3.0 12.3 + - + +
331A ALA* 3.1 11.4 + - - +
333A ARG* 1.3 74.1 - - - +
335A ILE* 1.3 64.2 + - - +
337A ARG* 2.8 45.9 + - - +
338A ALA* 3.0 22.3 + - - +
347A LEU* 3.7 7.5 - - + +
348A LYS 3.0 13.7 + - - -
349A ASN* 2.8 29.0 + - - +
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Residues in contact with ILE 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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30A VAL* 3.9 27.6 - - + -
45A LEU* 3.7 17.3 - - + -
72A GLY* 4.8 1.6 - - - -
73A ALA 4.1 15.9 - - - +
74A LEU* 3.6 28.7 - - + -
94A ILE* 4.3 17.2 - - + +
96A VAL* 3.4 23.1 - - + -
331A ALA 2.9 17.9 + - - +
332A ALA* 3.3 9.6 - - - +
334A GLU* 1.3 75.3 - - - +
336A ARG* 1.3 62.1 + - - +
338A ALA* 3.3 7.0 + - - +
339A ILE* 3.1 27.6 + - + +
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Residues in contact with ARG 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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43A PRO 5.1 1.6 + - - -
44A ILE* 2.8 39.6 + - - +
45A LEU* 4.0 10.8 - - + -
47A ASP* 2.8 41.9 + - - -
48A VAL* 3.7 21.3 - - + +
332A ALA 2.8 13.4 + - - +
333A ARG* 3.5 11.2 - - - +
335A ILE* 1.3 74.7 - - - +
337A ARG* 1.3 68.1 + - + +
339A ILE* 3.9 4.4 - - - +
340A THR* 2.9 36.9 + - - +
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Residues in contact with ARG 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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330A GLU* 2.9 28.1 + - - -
333A ARG* 2.8 37.2 + - + +
334A GLU* 2.8 53.8 + - - +
336A ARG* 1.3 76.3 - - + +
338A ALA* 1.3 58.7 + - - +
340A THR* 5.0 1.8 - - - -
341A GLY* 2.9 28.3 + - - +
346A SER* 3.4 37.0 + - - +
347A LEU* 4.7 0.7 - - + -
348A LYS* 3.7 16.2 - - - +
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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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93A ARG* 5.4 1.6 + - - -
94A ILE* 3.8 33.4 - - + -
334A GLU 3.0 12.3 + - - +
335A ILE 3.4 9.0 - - - +
336A ARG 3.1 0.2 - - - -
337A ARG* 1.3 75.6 - - - +
339A ILE* 1.3 65.0 + - + +
341A GLY 3.3 16.7 - - - +
342A ARG 5.4 0.4 - - - -
343A ILE* 4.0 27.5 - - + +
347A LEU* 4.0 9.6 - - + +
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Residues in contact with ILE 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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28A PRO* 3.9 21.5 - - + -
30A VAL* 3.9 16.4 - - + -
48A VAL* 3.7 37.2 - - + +
49A ALA* 3.9 16.8 - - + -
71A VAL* 5.6 8.5 - - + -
72A GLY* 6.6 0.4 - - - -
94A ILE* 6.2 1.8 - - + -
335A ILE* 3.1 22.2 + - + +
336A ARG* 4.0 4.0 - - - +
338A ALA* 1.3 79.3 - - + +
340A THR* 1.3 66.5 + - - +
341A GLY 3.7 2.9 + - - +
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Residues in contact with THR 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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48A VAL* 4.2 14.9 - - - +
336A ARG* 2.9 32.1 + - - +
337A ARG* 4.6 1.3 - - - -
339A ILE* 1.3 79.7 - - - +
341A GLY* 1.3 58.6 + - - +
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Residues in contact with GLY 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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93A ARG* 5.7 1.6 + - - -
337A ARG 2.9 16.2 + - - -
338A ALA 3.3 12.8 - - - +
339A ILE 4.2 2.4 - - - +
340A THR* 1.3 81.7 - - - +
342A ARG* 1.3 60.9 + - - -
343A ILE 4.2 0.3 + - - -
346A SER* 3.8 6.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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