Contacts of the helix formed by residues 322 - 338 (chain A) in PDB entry 4MQP
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 ASN 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ASN 3.3 14.6 + - - -
89A HIS* 3.1 23.7 + - + +
122A ASP* 5.3 1.6 - - - +
292A LEU* 5.0 3.7 - - + +
319A PHE* 3.0 23.2 + - + +
320A MET 3.2 0.4 - - - -
321A ALA* 1.3 75.3 - - - +
323A PRO* 1.4 63.1 - - - +
324A LEU* 3.6 6.1 + - - +
325A ALA* 2.9 35.2 + - + +
326A CYS* 2.9 26.9 + - - +
289B TYR 3.2 22.7 + - - -
290B LEU* 3.9 13.8 - - - +
291B SER* 5.3 1.7 + - - +
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Residues in contact with PRO 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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83A GLN* 3.7 14.5 - - - +
87A MET* 3.7 29.8 - - + +
88A ASN 3.7 0.9 - - - +
89A HIS* 3.6 32.1 - - + +
90A VAL 4.0 4.3 - - - +
97A HIS* 3.5 33.0 - - + +
99A PRO* 3.7 9.7 - - + +
321A ALA 3.4 6.7 - - - +
322A ASN* 1.4 81.7 - - - +
324A LEU* 1.3 56.3 + - - +
327A ALA* 2.9 31.9 + - - +
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Residues in contact with LEU 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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80A LEU* 3.4 32.7 - - + +
83A GLN* 4.0 10.3 - - + -
84A LEU* 3.7 43.3 - - + +
88A ASN* 3.2 23.3 + - + +
290A LEU* 3.9 0.2 - - - -
322A ASN* 3.3 7.1 - - - +
323A PRO* 1.3 74.2 - - - +
325A ALA* 1.3 66.9 + - - +
327A ALA* 3.3 1.4 + - - +
328A VAL* 3.2 18.5 + - - +
80B LEU* 3.9 21.8 - - + -
289B TYR* 3.7 20.9 - - + +
290B LEU* 3.8 15.5 - - + -
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Residues in contact with ALA 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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286A THR* 4.3 0.4 - - + +
290A LEU* 3.7 21.7 - - + +
291A SER 4.0 20.2 - - - +
292A LEU* 3.9 17.0 - - + -
322A ASN* 2.9 30.4 + - + +
324A LEU* 1.3 72.9 - - - +
326A CYS* 1.3 61.4 + - - +
328A VAL* 3.3 4.8 - - - +
329A SER* 2.8 28.9 + - - -
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Residues in contact with CYS 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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99A PRO* 3.6 26.0 - - + +
100A ALA* 4.1 14.6 - - - -
103A LEU* 3.9 22.8 - - + +
120A PHE* 4.4 6.5 - - - -
292A LEU* 4.1 7.6 - - - -
321A ALA* 3.6 26.5 - - - -
322A ASN 2.9 19.9 + - - +
325A ALA* 1.3 78.3 - - - +
327A ALA* 1.3 56.3 + - - +
329A SER* 3.2 2.9 + - - -
330A VAL* 3.0 33.4 + - - +
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Residues in contact with ALA 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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79A ALA* 3.9 14.4 - - + +
80A LEU* 5.2 0.4 - - - -
83A GLN* 3.6 33.2 - - + +
99A PRO* 4.0 6.7 - - + +
323A PRO 2.9 19.4 + - - +
324A LEU 3.3 3.8 + - - +
326A CYS* 1.3 76.4 - - - +
328A VAL* 1.3 62.3 + - - +
330A VAL* 3.4 8.8 + - - +
331A ALA* 3.3 21.0 + - - +
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Residues in contact with VAL 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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76A LEU* 3.9 28.2 - - + +
79A ALA* 4.5 7.2 - - - +
80A LEU* 4.2 12.3 - - + +
286A THR* 3.8 25.4 - - - +
289A TYR* 3.9 23.3 - - + -
290A LEU* 4.1 13.0 - - + -
324A LEU 3.2 11.0 + - - +
325A ALA* 3.3 17.7 - - - +
327A ALA* 1.3 80.1 - - - +
329A SER* 1.3 60.1 + - - +
331A ALA* 3.3 2.9 + - - +
332A SER* 2.9 26.3 + - - -
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Residues in contact with SER 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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103A LEU* 3.6 22.9 - - - -
285A LEU* 3.3 20.1 + - - -
286A THR* 3.2 24.1 - - - +
292A LEU* 3.4 6.1 - - - +
325A ALA 2.8 22.1 + - - -
326A CYS 3.2 5.1 + - - -
328A VAL* 1.3 75.7 - - - +
330A VAL* 1.3 59.5 + - - +
332A SER* 3.1 0.9 + - - -
333A VAL* 2.8 35.2 + - - +
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Residues in contact with VAL 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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99A PRO* 4.0 7.2 - - + +
102A ARG* 3.7 41.5 - - + +
103A LEU* 3.7 36.3 - - + +
106A LEU* 4.0 13.2 - - + -
326A CYS 3.0 19.3 + - - +
327A ALA* 3.6 10.8 - - - +
329A SER* 1.3 74.6 - - - +
331A ALA* 1.3 59.5 + - - +
333A VAL* 3.9 1.0 - - - +
334A GLU* 2.9 40.4 + - - +
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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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75A ALA* 4.2 7.2 - - + +
76A LEU* 3.6 14.3 - - + +
79A ALA* 3.4 33.2 - - + -
327A ALA 3.3 2.8 + - - +
328A VAL* 3.6 7.0 - - - +
329A SER 3.2 0.4 - - - -
330A VAL* 1.3 80.8 - - - +
332A SER* 1.3 57.1 + - - +
334A GLU* 3.5 7.5 + - - +
335A LEU* 2.9 30.8 + - - +
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Residues in contact with SER 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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68A ILE* 4.1 2.6 - - - +
69A HIS* 2.9 42.9 + - - -
76A LEU* 3.5 12.8 - - - +
284A ALA 3.8 6.6 + - - -
285A LEU 3.9 5.2 - - - -
286A THR 4.1 0.2 - - - -
287A GLY* 3.4 29.0 + - - -
328A VAL 2.9 16.9 + - - -
329A SER 3.1 4.9 + - - -
331A ALA* 1.3 76.4 - - - +
333A VAL* 1.3 61.6 + - - +
335A LEU 3.4 0.2 + - - -
336A LEU* 3.1 11.3 + - - +
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Residues in contact with VAL 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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103A LEU* 4.6 11.2 - - + -
106A LEU* 4.2 19.1 - - + -
107A LEU* 4.9 1.6 - - + -
110A ILE* 3.9 19.1 - - + -
260A PHE* 3.8 29.8 - - + -
285A LEU* 4.4 8.7 - - + +
329A SER 2.8 24.6 + - - +
330A VAL 3.9 3.1 - - - +
332A SER* 1.3 72.6 - - - +
334A GLU* 1.3 58.0 + - - +
336A LEU* 3.2 8.6 + - + +
337A LEU* 2.9 48.6 + - + +
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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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102A ARG* 3.0 30.7 + - - -
106A LEU* 4.0 22.3 - - + +
330A VAL* 2.9 28.3 + - - +
331A ALA* 4.0 6.6 - - - +
333A VAL* 1.3 76.0 - - - +
335A LEU* 1.3 57.3 + - - +
337A LEU* 3.9 7.5 - - + +
338A GLY* 2.8 29.8 + - - -
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Residues in contact with LEU 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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69A HIS* 3.5 31.4 - - + +
73A HIS* 3.5 42.8 - - + +
75A ALA* 4.7 8.7 - - + -
76A LEU* 4.2 9.0 - - + -
331A ALA 2.9 18.6 + - - +
332A SER 3.8 3.6 - - - +
333A VAL 3.2 0.2 - - - -
334A GLU* 1.3 77.7 - - - +
336A LEU* 1.3 61.3 + - - +
338A GLY* 3.7 5.2 + - - -
339A GLN* 2.9 30.1 + - + +
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Residues in contact with LEU 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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68A ILE* 4.7 3.4 - - + -
69A HIS* 3.6 13.6 - - + +
110A ILE* 6.4 0.2 - - + -
260A PHE* 3.5 43.1 - - + +
261A GLY* 5.0 0.2 - - - -
266A LEU* 3.9 18.4 - - + -
332A SER 3.1 13.8 + - - +
333A VAL* 3.5 11.2 - - + +
335A LEU* 1.3 77.4 - - - +
337A LEU* 1.3 62.2 + - + +
339A GLN* 3.2 23.5 - - - +
341A TRP* 3.4 41.8 - - + -
412A TYR* 3.8 30.3 - - + -
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Residues in contact with LEU 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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106A LEU* 4.1 14.1 - - + -
110A ILE* 3.7 23.8 - - + -
266A LEU* 4.0 35.4 - - + -
333A VAL* 2.9 36.7 + - + +
334A GLU* 3.9 5.6 - - + +
336A LEU* 1.3 78.3 - - + +
338A GLY* 1.3 58.0 + - - +
339A GLN 3.2 10.0 + - - +
341A TRP* 4.4 13.3 - - - +
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Residues in contact with GLY 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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334A GLU 2.8 15.8 + - - -
335A LEU* 4.2 3.4 - - - -
336A LEU 3.3 0.6 - - - -
337A LEU* 1.3 76.9 - - - +
339A GLN* 1.3 55.7 + - - +
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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