Contacts of the helix formed by residues 55 - 71 (chain A) in PDB entry 2C31
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 HIS 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.8 4.2 - - - +
53A PHE* 3.4 6.2 + - - +
54A ARG* 1.3 80.5 - - - +
56A GLU* 1.3 65.1 + - - +
57A GLN* 2.9 43.9 + - + +
58A HIS* 3.1 33.5 + + + +
59A ALA 3.6 6.2 + - - -
86A ASN* 3.3 32.7 + - + -
461A GLU* 3.0 2.5 + - - +
55B HIS* 5.5 3.8 + + - -
57B GLN* 2.9 25.2 + - - -
58B HIS* 5.1 1.1 - + - -
456B GLY 5.0 1.3 - - - +
457B PHE* 3.5 45.1 - + + +
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Residues in contact with GLU 56 (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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31A VAL* 3.6 26.3 - - + +
55A HIS* 1.3 71.8 + - - +
57A GLN* 1.3 63.1 + - - +
59A ALA* 3.1 7.2 + - - +
60A GLY* 2.9 20.4 + - - -
76A CYS* 4.3 3.5 - - - -
78A THR* 3.6 25.5 - - + -
79A VAL* 4.5 1.9 - - - +
83A GLY* 3.6 28.4 - - - +
86A ASN* 3.0 27.5 + - + -
87A GLY* 4.0 3.5 - - - +
457B PHE* 3.5 10.1 - - - -
1554B TZD 2.6 35.1 + - - +
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Residues in contact with GLN 57 (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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55A HIS* 2.9 26.0 + - + +
56A GLU* 1.3 78.7 - - - +
58A HIS* 1.3 73.0 + - + +
60A GLY 3.3 0.2 + - - -
61A TYR* 3.0 43.6 + - + -
86A ASN* 3.5 10.9 + - - +
89A THR* 3.0 19.4 + - - +
90A SER* 2.5 32.3 + - - +
429A GLY* 5.7 1.0 - - - -
55B HIS* 2.9 25.0 + - - -
86B ASN* 2.7 28.7 + - - -
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Residues in contact with HIS 58 (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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53A PHE* 3.7 6.2 - - + -
55A HIS* 3.1 25.6 + - + +
56A GLU 3.1 0.6 - - - -
57A GLN* 1.3 96.2 + - - +
59A ALA* 1.3 63.2 + - - +
60A GLY 3.1 1.1 - - - -
61A TYR* 3.3 5.5 + - - +
62A ALA* 3.0 23.6 + - - +
429A GLY 3.6 17.7 + - - -
433A GLY* 3.7 15.1 + - - -
457A PHE 3.1 27.9 + - - -
458A SER* 3.4 14.7 - - - -
461A GLU* 3.4 46.0 - - + -
55B HIS* 5.2 1.6 - - - -
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Residues in contact with ALA 59 (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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29A TYR* 3.5 10.5 - - - +
30A GLY* 3.5 39.3 - - - +
53A PHE* 3.6 26.3 - - + -
55A HIS 3.6 3.0 + - - -
56A GLU* 3.1 12.0 + - - +
58A HIS* 1.3 77.9 - - - +
60A GLY* 1.3 58.3 + - - +
62A ALA* 3.3 3.6 - - - +
63A ALA* 3.0 24.8 + - - +
76A CYS* 4.1 5.1 - - - -
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Residues in contact with GLY 60 (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 GLU 2.9 12.8 + - - -
58A HIS 3.1 0.2 - - - -
59A ALA* 1.3 77.0 - - - +
61A TYR* 1.3 64.5 + - - +
63A ALA* 3.2 2.8 + - - +
64A SER* 3.0 19.9 + - - -
76A CYS* 3.8 15.0 - - - -
87A GLY 5.1 0.9 - - - -
90A SER* 3.5 22.4 - - - -
101A MET* 3.6 14.5 - - - +
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Residues in contact with TYR 61 (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 GLN* 3.0 52.8 + - + +
58A HIS* 3.3 12.1 + - - +
60A GLY* 1.3 75.5 - - - +
62A ALA* 1.3 63.1 + - - +
64A SER* 2.9 20.1 + - - -
65A ILE 3.2 5.9 + - - -
89A THR* 4.7 3.9 + - - -
90A SER* 3.7 21.8 - - - -
93A HIS* 3.7 33.1 - + + +
427A VAL* 3.5 22.2 - - + +
428A MET 4.9 1.1 + - - -
429A GLY* 3.2 33.7 - - - -
430A ILE* 3.8 13.9 - - + +
433A GLY* 4.7 2.5 - - - -
434A TYR* 3.3 22.8 - - + -
82B PRO* 5.6 1.7 - - - +
86B ASN* 4.9 2.6 + - - -
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Residues in contact with ALA 62 (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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29A TYR* 3.9 12.6 - - + -
53A PHE* 3.6 19.7 - - + -
58A HIS 3.0 14.1 + - - +
59A ALA 3.3 10.3 - - - +
61A TYR* 1.3 78.7 - - - +
63A ALA* 1.3 63.4 + - - +
65A ILE* 4.4 0.4 - - - -
66A ALA* 3.0 19.4 + - - +
433A GLY 3.4 24.4 + - - +
437A ALA* 3.1 17.7 - - + +
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Residues in contact with ALA 63 (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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29A TYR* 3.9 11.6 - - + -
59A ALA 3.0 14.0 + - - +
60A GLY 3.6 7.9 - - - +
62A ALA* 1.3 75.1 - - - +
64A SER* 1.3 63.5 + - - +
66A ALA 3.3 0.5 + - - -
67A GLY* 3.1 17.3 + - - -
74A GLY* 3.3 35.8 + - - +
75A VAL 3.9 17.7 - - - +
76A CYS* 4.0 7.6 - - + +
100A PRO 4.2 0.3 - - - +
101A MET* 4.2 6.5 - - + -
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Residues in contact with SER 64 (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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60A GLY 3.0 13.4 + - - -
61A TYR* 2.9 16.3 + - - -
62A ALA 3.2 0.2 - - - -
63A ALA* 1.3 77.6 - - - +
65A ILE* 1.3 61.3 + - - +
67A GLY* 3.3 2.6 + - - -
68A TYR 3.2 15.2 + - - -
90A SER 4.7 0.4 - - - -
93A HIS* 3.5 26.4 + - - -
94A ALA* 3.8 25.6 - - - -
99A PHE* 3.4 19.2 - - - +
100A PRO 4.4 0.2 - - - +
101A MET* 3.9 12.7 - - - -
434A TYR* 3.9 3.5 + - - -
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Residues in contact with ILE 65 (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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61A TYR 3.2 3.0 + - - +
62A ALA 3.4 10.5 - - - +
64A SER* 1.3 76.3 + - - +
66A ALA* 1.3 62.3 + - - +
67A GLY 3.1 1.8 - - - -
68A TYR* 3.1 19.9 + - + -
69A ILE* 2.9 40.6 + - + +
99A PHE* 4.1 9.0 - - + -
249A MET* 4.2 4.0 - - + -
420A LEU* 3.7 39.5 - - + -
434A TYR* 3.7 54.5 - - + +
437A ALA* 3.4 18.2 - - + -
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Residues in contact with ALA 66 (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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29A TYR* 3.7 27.4 - - + +
62A ALA 3.0 17.5 + - - +
63A ALA 3.6 5.4 - - - +
64A SER 3.3 0.2 - - - -
65A ILE* 1.3 78.2 - - - +
67A GLY* 1.3 62.7 + - - +
69A ILE* 3.5 4.3 + - - +
70A GLU* 3.0 35.5 + - - +
72A LYS 4.5 1.6 - - - -
74A GLY* 4.3 6.5 - - - -
437A ALA* 4.3 2.0 - - + -
441A VAL* 4.0 16.4 - - + -
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ALA 3.1 10.3 + - - -
64A SER 3.3 1.5 + - - -
65A ILE 3.1 0.2 - - - -
66A ALA* 1.3 77.2 - - - +
68A TYR* 1.3 55.9 + - - +
71A GLY 2.9 24.8 + - - -
72A LYS 3.2 19.7 - - - -
74A GLY 3.9 1.3 - - - +
100A PRO* 3.3 35.9 - - - +
226A TYR* 3.5 1.9 - - - -
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Residues in contact with TYR 68 (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 SER 3.2 9.4 + - - +
65A ILE* 3.1 27.3 + - + +
67A GLY* 1.3 78.2 - - - +
69A ILE* 1.3 65.9 + - + +
71A GLY 4.1 1.2 + - - -
99A PHE* 3.4 37.2 - + + -
100A PRO* 4.1 1.2 - - - +
222A LYS* 3.9 21.6 - - + +
225A ALA* 3.4 21.7 - - - +
226A TYR* 3.4 38.4 - + + +
228A GLN* 5.1 0.9 - - - +
249A MET* 3.5 36.6 + - + +
417A ARG* 3.9 33.2 - - + +
419A ARG 4.8 0.6 + - - -
420A LEU* 4.0 14.4 - - + -
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Residues in contact with ILE 69 (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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65A ILE* 2.9 34.2 + - + +
66A ALA 4.0 2.5 - - - +
68A TYR* 1.3 87.0 - - + +
70A GLU* 1.3 58.5 + - + +
228A GLN* 3.4 16.3 - - - +
395A SER* 5.4 1.1 - - - +
417A ARG* 4.2 26.0 + - + +
420A LEU* 4.3 13.9 - - + -
438A ALA* 4.1 19.7 - - + +
441A VAL* 3.9 30.7 - - + -
442A THR* 4.6 12.6 - - + -
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Residues in contact with GLU 70 (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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49A ARG* 5.9 0.3 + - - -
66A ALA* 3.0 20.8 + - - +
69A ILE* 1.3 82.0 - - + +
71A GLY* 1.3 60.6 + - - +
72A LYS* 3.4 38.7 + - + +
228A GLN* 3.9 10.8 - - - +
441A VAL* 3.6 42.4 - - + +
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Residues in contact with GLY 71 (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 GLY 2.9 14.6 + - - -
68A TYR 4.1 1.4 + - - -
69A ILE 3.8 1.0 - - - -
70A GLU* 1.3 77.8 - - - +
72A LYS* 1.3 59.5 + - - +
100A PRO* 4.5 0.2 - - - -
157A VAL* 4.0 10.6 - - - +
226A TYR* 3.8 29.5 + - - -
228A GLN* 4.8 3.1 + - - -
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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
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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