Contacts of the helix formed by residues 313 - 328 (chain A) in PDB entry 5UC7
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 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A SER 3.2 17.0 + - - -
77A HIS* 2.9 33.6 + - - +
281A MET* 3.5 17.2 - - - +
283A LEU* 5.1 5.7 - - + +
310A PHE* 3.0 26.4 + - + +
311A MET 3.2 0.6 - - - -
312A GLY* 1.3 74.0 - - - +
314A PRO* 1.3 69.3 - - - +
315A LEU* 3.6 4.2 - - - +
316A ALA* 3.1 27.8 + - + +
317A CYS* 3.0 19.6 + - - -
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Residues in contact with PRO 314 (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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71A GLN* 3.6 25.6 - - - +
75A MET* 3.7 15.7 - - + +
76A SER 3.8 5.6 - - - +
77A HIS* 3.7 17.3 - - - +
78A VAL 3.8 15.7 - - - +
85A HIS* 3.5 32.8 - - + +
87A PRO* 3.6 9.6 - - + +
312A GLY 3.3 8.5 - - - +
313A ASN* 1.3 82.4 - - - +
315A LEU* 1.3 57.6 + - - +
317A CYS 3.3 0.3 + - - -
318A ALA* 2.8 32.1 + - - +
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Residues in contact with LEU 315 (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 MET* 3.6 49.8 - - + +
71A GLN* 3.9 11.6 - - + +
72A ILE* 4.0 21.1 - - + -
76A SER* 3.0 31.6 + - - +
281A MET* 3.7 23.6 - - + -
313A ASN* 3.3 7.1 - - - +
314A PRO* 1.3 76.0 - - - +
316A ALA* 1.3 64.7 + - - +
318A ALA* 3.2 1.6 + - - +
319A VAL* 3.1 21.0 + - - +
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Residues in contact with ALA 316 (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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277A THR* 4.0 1.1 - - + +
281A MET* 3.7 23.8 - - + -
282A THR 3.9 18.6 - - - +
283A LEU* 3.8 21.5 - - + +
313A ASN* 3.1 24.6 + - + +
315A LEU* 1.3 76.1 - - - +
317A CYS* 1.3 63.4 + - - +
319A VAL* 3.4 4.9 - - - +
320A ALA* 2.9 24.8 + - - +
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Residues in contact with CYS 317 (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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87A PRO* 3.6 28.3 - - + +
88A ALA* 3.9 13.5 - - - -
91A LEU* 3.8 25.9 - - + +
108A LEU* 4.0 8.7 - - - -
283A LEU* 4.2 7.6 - - - -
312A GLY 3.6 19.7 - - - -
313A ASN 3.0 19.6 + - - +
314A PRO* 4.3 0.4 - - + -
316A ALA* 1.3 79.1 - - - +
318A ALA* 1.4 57.7 + - - +
320A ALA* 3.3 2.9 + - - +
321A ASN* 2.9 34.3 + - - +
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Residues in contact with ALA 318 (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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67A ALA* 4.0 14.3 - - + +
71A GLN* 3.6 33.2 - - + +
87A PRO* 3.8 4.7 - - + +
314A PRO 2.8 21.3 + - - +
315A LEU* 3.2 3.3 + - + +
317A CYS* 1.4 74.1 - - - +
319A VAL* 1.3 60.5 + - - +
321A ASN* 3.4 13.2 + - - +
322A ALA* 3.2 20.3 + - - +
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Residues in contact with VAL 319 (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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64A LEU* 4.0 27.6 - - + +
67A ALA* 4.7 2.2 - - - -
68A MET* 3.7 30.0 - - + +
277A THR* 3.9 15.3 - - - +
280A THR* 3.2 27.8 - - + +
281A MET* 4.1 8.7 - - - -
315A LEU 3.1 13.7 + - - +
316A ALA* 3.4 15.0 - - - +
318A ALA* 1.3 74.3 - - - +
320A ALA* 1.3 68.7 + - - +
322A ALA* 3.3 4.0 + - - +
323A SER* 3.0 21.8 + - - -
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Residues in contact with ALA 320 (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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91A LEU* 3.9 18.6 - - + -
276A LEU* 3.3 29.2 - - + +
277A THR* 4.0 2.9 - - - +
283A LEU* 4.1 13.0 - - + -
316A ALA 2.9 19.7 + - - +
317A CYS 3.6 4.3 - - - +
319A VAL* 1.3 76.5 - - - +
321A ASN* 1.3 57.1 + - - +
323A SER* 3.2 2.3 + - - -
324A LEU* 2.8 36.8 + - - +
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Residues in contact with ASN 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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87A PRO* 3.1 32.5 + - - +
90A GLU* 3.5 38.8 + - - +
91A LEU* 3.0 30.5 + - - +
94A LYS* 4.0 8.9 - - - +
317A CYS 2.9 18.2 + - - -
318A ALA* 3.5 10.8 - - - +
319A VAL 3.3 0.4 - - - -
320A ALA* 1.3 77.2 - - - +
322A ALA* 1.3 57.7 + - - +
324A LEU* 3.4 2.2 + - - +
325A THR* 2.9 33.6 + - - -
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Residues in contact with ALA 322 (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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63A GLN* 4.0 10.8 - - + +
64A LEU* 3.7 14.1 - - + -
67A ALA* 3.5 31.6 - - + -
318A ALA 3.2 3.6 + - - -
319A VAL 3.7 7.2 - - - +
320A ALA 3.3 0.4 - - - -
321A ASN* 1.3 78.6 - - - +
323A SER* 1.3 57.9 + - - +
325A THR* 3.3 8.5 + - - -
326A LEU* 3.0 31.0 + - - +
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Residues in contact with SER 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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56A ILE* 4.5 1.6 - - - +
57A HIS* 2.9 32.0 + - - -
64A LEU* 3.4 14.5 - - - +
275A ALA 3.7 7.4 + - - -
276A LEU 3.9 4.8 + - - -
278A GLY* 3.4 24.3 + - - -
319A VAL 3.0 14.3 + - - -
320A ALA 3.5 7.6 - - - -
322A ALA* 1.3 78.5 - - - +
324A LEU* 1.3 63.2 + - - +
326A LEU* 3.2 2.8 + - - -
327A LEU* 3.1 20.3 + - - +
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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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91A LEU* 3.5 31.9 - - + -
94A LYS* 3.8 31.6 - - + -
95A LEU* 4.3 10.1 - - + -
98A MET* 4.0 15.8 - - + +
251A PHE* 3.5 36.8 - - + -
275A ALA 6.0 0.2 - - - +
276A LEU* 4.8 8.1 - - + +
320A ALA 2.8 21.1 + - - +
321A ASN 3.7 3.6 - - - +
323A SER* 1.3 74.1 - - - +
325A THR* 1.3 64.1 + - - +
327A LEU* 3.2 12.5 + - + +
328A GLU* 3.1 26.7 + - - +
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Residues in contact with THR 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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90A GLU* 4.6 2.3 + - - -
94A LYS* 3.5 17.2 + - - +
321A ASN 2.9 20.2 + - - -
322A ALA* 3.5 9.1 - - - +
324A LEU* 1.3 74.5 - - - +
326A LEU* 1.3 67.8 + - + +
328A GLU* 3.2 30.3 + - - +
329A SER* 3.8 2.8 + - - -
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Residues in contact with LEU 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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57A HIS* 3.6 37.5 - - + +
61A HIS* 3.5 43.7 - - + +
63A GLN* 4.3 17.3 - - + +
64A LEU* 4.0 15.0 - - + -
322A ALA 3.0 14.3 + - - +
323A SER 3.2 7.8 + - - +
325A THR* 1.3 79.0 - - + +
327A LEU* 1.3 62.7 + - - +
329A SER* 3.1 23.9 + - - -
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Residues in contact with LEU 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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56A ILE* 3.9 13.7 - - + -
57A HIS* 3.8 19.3 - - + -
98A MET* 5.0 2.5 - - + -
251A PHE* 4.0 39.7 - - + +
257A LEU* 4.4 11.7 - - + -
275A ALA 5.9 0.2 - - - +
323A SER* 3.1 16.9 + - - +
324A LEU* 3.2 16.8 + - + +
326A LEU* 1.3 76.6 - - - +
328A GLU* 1.3 56.7 + - - +
329A SER 3.0 0.2 - - - -
330A GLY* 2.8 20.1 + - - -
332A TRP* 3.2 48.7 + - + +
403A TYR* 4.3 5.2 - - + -
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Residues in contact with GLU 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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94A LYS* 3.6 27.0 + - - +
324A LEU* 3.1 15.7 + - - +
325A THR* 3.4 24.0 + - - +
326A LEU 3.2 0.8 - - - -
327A LEU* 1.3 72.4 - - - +
329A SER* 1.3 64.9 + - - +
330A GLY* 3.0 1.7 + - - -
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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