Contacts of the helix formed by residues 52 - 73 (chain D) in PDB entry 6A5T
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 52 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ALA 4.3 0.4 + - - -
51D LEU* 1.3 73.0 - - - +
53D LEU* 1.3 68.9 + - - +
54D SER* 3.9 1.9 + - - -
55D GLU* 3.3 36.7 + - - +
56D SER* 2.9 26.7 + - - -
124D VAL* 6.1 0.7 - - - +
142D ILE* 5.1 2.2 - - - -
143D ALA* 3.7 19.2 - - - +
146D SER* 3.6 30.3 + - - -
147D SER* 5.3 0.2 - - - -
2G PHE* 5.4 2.0 - - - -
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D SER* 1.3 78.1 - - - +
54D SER* 1.3 59.7 + - - +
56D SER* 4.9 1.3 - - - -
57D ARG* 2.8 34.9 + - - +
108D TYR 5.2 0.9 - - - +
109D LEU* 3.7 29.3 - - + +
112D PHE* 3.4 43.7 - - + +
113D ALA* 5.2 4.3 - - - -
114D ARG* 5.5 3.6 - - + +
143D ALA 5.2 0.2 + - - -
146D SER* 4.4 13.0 + - - +
147D SER* 4.1 23.8 - - - +
1G MET* 6.5 1.1 - - - -
2G PHE* 5.0 9.4 - - + -
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Residues in contact with SER 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D SER* 3.4 4.7 + - - -
53D LEU* 1.3 76.3 - - - +
55D GLU* 1.3 61.3 + - - +
57D ARG* 3.7 5.6 - - - +
58D LEU* 2.9 37.8 + - - +
113D ALA* 5.4 0.6 - - - +
114D ARG* 4.1 6.2 + - - +
115D PHE* 2.7 61.4 + - - +
121D CYS* 4.7 10.1 - - - -
146D SER* 4.5 4.5 + - - -
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Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ALA 4.2 10.7 - - - +
51D LEU* 4.2 11.9 - - + +
52D SER* 3.3 31.4 + - - +
53D LEU 3.5 0.2 - - - -
54D SER* 1.3 76.9 - - - +
56D SER* 1.3 65.5 + - - +
58D LEU* 3.3 5.0 + - - +
59D LEU* 3.0 31.0 + - + +
121D CYS* 3.7 29.8 - - - +
124D VAL* 5.1 6.5 - - + +
125D ASP* 5.2 3.6 - - - +
129D HIS* 3.4 29.2 + - - -
142D ILE* 5.5 0.2 - - - +
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Residues in contact with SER 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 2.9 38.1 - - - +
52D SER 2.9 13.9 + - - -
53D LEU* 4.2 1.6 - - - -
55D GLU* 1.3 78.2 - - - +
57D ARG* 1.3 58.5 + - - +
59D LEU* 3.2 10.7 + - - +
60D ILE* 2.9 39.5 + - - +
109D LEU* 5.4 2.0 - - - -
2G PHE* 3.7 24.4 - - - +
77G VAL* 5.3 2.7 - - - -
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Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LEU* 2.8 22.6 + - - +
54D SER* 3.7 5.2 - - - +
55D GLU 3.2 0.2 - - - -
56D SER* 1.3 77.1 - - - +
58D LEU* 1.3 67.6 + - - +
60D ILE* 3.9 4.7 - - - +
61D ARG* 2.9 79.3 + - + +
109D LEU* 3.9 31.0 + - + +
110D ASN* 4.6 12.3 + - - +
113D ALA* 3.7 26.0 - - - +
115D PHE 5.2 1.5 + - - -
116D LYS* 3.5 51.2 + - - +
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Residues in contact with LEU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D SER* 2.9 22.5 + - - +
55D GLU* 3.6 5.2 - - - +
57D ARG* 1.3 84.4 - - - +
59D LEU* 1.3 64.8 + - + +
61D ARG* 3.8 6.3 - - - +
62D GLU* 2.9 28.3 + - - +
115D PHE 5.1 0.7 - - - +
116D LYS* 3.8 24.9 - - - +
117D ASP* 3.8 22.4 - - - +
118D GLU* 3.8 16.8 - - + +
121D CYS* 3.8 26.7 - - + -
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 4.6 18.2 - - + -
55D GLU* 3.0 24.3 + - + +
56D SER* 3.2 10.3 + - - +
58D LEU* 1.3 78.0 - - + +
60D ILE* 1.3 59.1 + - + +
62D GLU* 4.1 2.4 - - + +
63D ALA* 2.9 33.5 + - - +
4G LEU* 4.7 15.9 - - + -
49G LEU* 4.0 26.6 - - + +
77G VAL* 5.7 3.6 - - + -
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Residues in contact with ILE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D SER 2.9 22.5 + - - +
57D ARG* 3.9 3.8 - - - +
59D LEU* 1.3 75.3 - - + +
61D ARG* 1.3 62.3 + - + +
63D ALA* 3.8 3.7 - - - +
64D LEU* 2.9 50.7 + - + +
102D VAL* 6.5 0.2 - - + -
105D THR* 6.1 0.9 - - + -
106D LEU* 5.5 8.5 - - + -
109D LEU* 4.2 24.2 - - + -
2G PHE* 4.4 9.6 - - + -
46G VAL* 4.6 9.9 - - + -
47G THR* 4.1 23.8 - - + +
49G LEU* 5.6 0.7 - - - -
77G VAL* 4.3 26.7 - - + -
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ARG* 2.9 74.7 + - + +
58D LEU* 3.8 6.7 - - - +
60D ILE* 1.3 80.9 - - + +
62D GLU* 1.3 62.7 + - - +
64D LEU* 3.7 1.7 - - - +
65D LYS* 3.0 53.4 + - - +
84D ILE* 4.3 16.0 + - - +
85D ASP 5.0 4.0 + - - -
86D ASP* 4.2 17.4 + - - +
89D LEU* 4.0 22.0 - - + +
106D LEU* 6.0 4.3 - - + -
110D ASN* 5.6 1.8 + - - -
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LEU 2.9 18.0 + - - +
59D LEU* 4.3 3.4 - - + +
61D ARG* 1.3 76.7 - - - +
63D ALA* 1.3 63.3 + - - +
65D LYS* 3.2 26.9 + - - +
66D ALA* 2.9 34.8 + - + +
69D ARG* 4.8 8.0 + - - -
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU 2.9 20.3 + - - +
60D ILE* 3.8 4.7 - - - +
62D GLU* 1.3 76.9 - - - +
64D LEU* 1.3 62.5 + - - +
66D ALA* 3.9 3.5 - - - +
67D ARG* 2.9 31.1 + - - +
47G THR* 5.7 2.0 - - - +
48G VAL 4.0 15.0 - - - +
49G LEU* 3.8 23.6 - - + -
50G ASP 5.0 3.8 - - - +
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ILE* 2.9 42.0 + - + +
61D ARG* 4.8 0.4 - - + -
63D ALA* 1.3 75.6 - - + +
65D LYS* 1.3 58.3 + - - +
67D ARG* 4.5 6.1 - - - +
68D SER 2.9 24.9 + - - -
89D LEU* 3.2 44.2 - - + +
90D ALA* 4.6 3.8 - - - +
92D VAL* 3.2 38.9 - - + +
93D THR* 3.9 24.2 - - + -
102D VAL* 5.3 6.7 - - + -
106D LEU* 5.3 7.0 - - + -
47G THR* 4.4 9.6 - - + -
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Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ARG* 3.0 59.2 + - - +
62D GLU* 3.2 35.1 + - - +
64D LEU* 1.3 74.5 - - - +
66D ALA* 1.3 60.7 + - - +
68D SER* 3.4 4.5 + - - +
69D ARG* 2.9 36.5 + - - +
84D ILE 6.1 2.9 - - - +
89D LEU* 3.6 21.3 - - + -
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLU* 2.9 27.9 + - + +
63D ALA* 4.0 3.6 - - - +
65D LYS* 1.3 77.0 - - - +
67D ARG* 1.3 57.0 + - - +
69D ARG* 3.3 27.3 + - - +
70D ALA* 2.9 28.3 + - - +
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ALA* 2.9 23.3 + - - +
64D LEU* 4.7 8.3 - - - +
66D ALA* 1.3 78.1 - - - +
68D SER* 1.3 56.6 + - - +
70D ALA* 3.2 9.3 + - - +
71D ARG* 2.8 35.6 + - - +
92D VAL* 3.4 33.5 + - + +
93D THR* 4.3 3.0 - - - +
31G LEU* 4.0 7.5 - - - +
35G GLU* 2.6 31.5 + - - -
47G THR* 4.3 3.8 - - - -
48G VAL* 2.3 52.1 + - - +
50G ASP 5.7 0.2 - - - +
51G GLY* 4.3 13.5 - - - +
52G MET* 3.5 33.0 - - + +
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Residues in contact with SER 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LEU 2.9 10.3 + - - -
65D LYS* 3.9 5.8 - - - -
67D ARG* 1.3 74.8 - - - +
69D ARG* 1.3 61.4 + - - +
71D ARG* 2.8 32.8 + - - +
72D ASN* 2.9 23.2 + - - +
88D GLU* 5.0 10.7 + - - +
89D LEU* 5.8 0.7 - - - -
91D LYS* 5.6 6.2 - - - +
92D VAL* 3.4 26.7 - - - +
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLU* 4.8 8.5 + - - -
65D LYS* 2.9 25.5 + - - +
66D ALA* 3.7 31.7 + - - +
68D SER* 1.3 76.9 - - - +
70D ALA* 1.3 51.8 + - - +
72D ASN* 3.5 1.7 - - - +
73D GLY 2.5 28.9 + - - -
74D GLY* 3.2 17.5 + - - +
75D VAL 3.2 43.7 + - - +
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ALA 2.9 14.0 + - - +
67D ARG* 3.4 9.0 - - - +
69D ARG* 1.3 75.4 - - - +
71D ARG* 1.3 64.9 + - - +
72D ASN 3.3 0.3 + - - -
73D GLY* 3.4 11.2 + - - +
52G MET* 4.0 26.7 - - + -
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Residues in contact with ARG 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ARG* 2.8 19.7 + - + +
68D SER* 2.8 28.3 + - - +
70D ALA* 1.3 78.3 - - - +
72D ASN* 1.3 62.8 + - - +
91D LYS* 4.4 9.2 + - - +
92D VAL* 2.2 51.0 + - - +
93D THR 3.7 7.5 + - - -
94D SER* 3.9 12.1 + - - -
28G GLU* 5.8 2.5 + - - -
31G LEU* 4.5 12.4 - - - +
52G MET* 5.8 5.6 - - - -
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Residues in contact with ASN 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D SER* 2.9 21.7 + - - +
69D ARG* 3.5 3.4 - - - +
71D ARG* 1.3 82.0 - - - +
73D GLY* 1.3 64.7 + - - +
74D GLY 3.8 0.2 - - - -
75D VAL* 4.2 25.2 - - + +
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Residues in contact with GLY 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ARG 2.5 16.1 + - - -
70D ALA* 3.4 12.2 + - - -
72D ASN* 1.3 76.6 - - - +
74D GLY* 1.3 58.5 + - - -
75D VAL* 4.6 2.1 - - - +
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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