Contacts of the helix formed by residues 72 - 90 (chain X) in PDB entry 5A31
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 72 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71X PHE* 1.3 73.5 - - - +
73X PRO* 1.3 64.5 - - - +
74X PRO* 3.4 12.3 - - - +
75X GLN* 2.6 63.7 + - - +
76X LYS* 2.8 10.1 + - - -
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Residues in contact with PRO 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492H PRO 6.0 1.8 - - - +
71X PHE 3.7 3.7 - - - +
72X SER* 1.3 84.0 - - - +
74X PRO* 1.3 70.7 - - + +
76X LYS* 3.2 21.2 + - + +
77X TYR* 3.1 21.1 + - - +
106X GLN* 4.0 10.9 - - + +
109X ALA* 6.0 4.7 - - + -
110X LEU 4.0 17.7 - - - +
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Residues in contact with PRO 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72X SER* 3.4 14.1 - - - +
73X PRO* 1.3 98.8 - - + +
75X GLN* 1.3 61.8 + - + +
77X TYR* 3.3 10.2 + - + +
78X GLN* 3.1 32.6 + - - +
110X LEU 4.0 14.6 - - - +
132X LEU* 5.6 9.4 - - + +
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Residues in contact with GLN 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X ASN 5.6 5.4 - - - +
38X ILE* 4.0 31.7 - - + +
39X ASP* 5.8 2.4 + - - +
70X LEU 4.8 0.5 - - - +
71X PHE* 3.5 18.2 - - + +
72X SER* 2.6 47.7 + - - +
74X PRO* 1.3 76.5 - - + +
76X LYS* 1.3 60.3 + - - +
78X GLN* 3.2 11.5 + - - +
79X LEU* 3.0 23.5 + - - +
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Residues in contact with LYS 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492H PRO 5.5 1.2 + - - -
493H SER* 6.2 0.4 - - - -
494H HIS* 3.8 30.5 + - - -
61X LEU* 5.2 3.6 - - + +
64X SER* 3.7 25.0 + - - +
68X PRO* 4.6 4.0 - - - +
69X GLU* 4.0 16.9 - - - +
71X PHE* 3.1 30.5 - - + +
72X SER 2.8 11.2 + - - +
73X PRO* 3.2 17.8 + - + +
75X GLN* 1.3 77.2 - - - +
77X TYR* 1.3 61.6 + - - +
79X LEU* 3.2 10.1 + - - +
80X LEU* 2.9 22.5 + - - +
106X GLN* 2.9 35.7 + - - +
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Residues in contact with TYR 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73X PRO 3.1 12.5 + - - +
74X PRO* 3.3 13.7 - - + +
76X LYS* 1.3 75.0 - - - +
78X GLN* 1.3 73.7 + - + +
80X LEU* 3.2 6.0 + - - +
81X VAL* 2.9 45.1 + - + +
103X ALA* 3.4 26.0 - - + -
104X LEU* 4.8 2.1 - - + +
106X GLN* 3.3 14.0 - - + +
107X LYS* 3.5 42.3 - - + +
132X LEU* 4.7 7.6 - - + -
133X PRO* 2.9 36.8 + - + -
135X GLU* 3.9 10.7 + - - -
138X VAL* 3.7 16.8 - - + +
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Residues in contact with GLN 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38X ILE* 3.8 22.2 - - + +
39X ASP* 5.7 1.0 + - - +
42X ARG* 4.4 19.9 + - - +
74X PRO* 3.1 19.7 + - - +
75X GLN* 3.6 11.1 - - - +
77X TYR* 1.3 84.2 - - + +
79X LEU* 1.3 64.2 + - - +
81X VAL* 3.1 6.1 + - - +
82X TYR* 2.9 51.9 + - + -
132X LEU* 4.3 24.1 + - + +
133X PRO* 4.4 16.8 - - + -
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Residues in contact with LEU 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X ILE* 3.8 24.2 - - + +
41X VAL* 5.5 4.7 - - + -
57X SER* 3.5 39.9 - - - +
60X LEU* 3.8 35.7 - - + +
61X LEU* 4.1 15.9 - - + +
64X SER* 4.9 3.6 - - - -
71X PHE* 4.7 11.7 - - + -
75X GLN 3.0 13.4 + - - +
76X LYS* 3.4 13.2 - - - +
78X GLN* 1.3 76.9 - - - +
80X LEU* 1.3 57.6 + - - +
82X TYR* 3.3 7.0 + - - +
83X HIS* 2.8 27.0 + - - +
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Residues in contact with LEU 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X LEU* 4.1 26.4 - - + +
76X LYS 2.9 11.5 + - - +
77X TYR 3.2 8.5 + - - +
79X LEU* 1.3 76.1 - - - +
81X VAL* 1.3 56.8 + - - +
83X HIS* 3.2 4.5 + - + +
84X ALA* 2.8 31.8 + - - +
99X LYS* 3.8 35.2 - - + +
102X MET* 3.5 23.1 - - + +
103X ALA* 3.4 38.4 - - + +
106X GLN* 4.2 15.0 - - - +
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Residues in contact with VAL 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77X TYR* 2.9 51.7 + - + +
78X GLN 3.6 5.8 - - - +
80X LEU* 1.3 77.0 - - - +
82X TYR* 1.3 59.8 + - + +
84X ALA* 3.2 6.8 + - - +
85X ASP* 3.0 46.7 + - - +
100X TYR* 4.9 4.7 - - + -
103X ALA* 4.1 10.8 - - + -
133X PRO* 3.6 29.2 - - + -
138X VAL* 4.2 16.2 - - + -
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Residues in contact with TYR 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X ILE* 4.9 3.6 - - + -
41X VAL* 4.2 27.6 - - + -
42X ARG* 3.5 47.3 - - + +
45X ALA* 3.9 24.0 - - + -
53X VAL* 4.3 10.1 - - + +
57X SER* 5.0 1.8 - - - -
78X GLN* 2.9 44.5 + - + +
79X LEU* 3.8 4.7 - - - +
81X VAL* 1.3 76.4 - - + +
83X HIS* 1.3 64.7 + - - +
85X ASP* 3.4 20.4 - - - +
86X SER* 3.1 21.7 + - - -
132X LEU 4.9 1.0 + - - -
133X PRO* 4.2 28.3 - - + +
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Residues in contact with HIS 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54X ARG* 4.0 15.0 + - + -
57X SER* 2.9 27.4 + - - +
58X SER* 3.7 30.0 + - - -
61X LEU* 3.6 19.4 - - + +
79X LEU 2.8 17.6 + - - +
80X LEU* 3.5 4.0 - - - +
82X TYR* 1.3 77.6 - - - +
84X ALA* 1.3 60.8 + - - +
86X SER* 2.2 27.5 + - - -
87X LEU* 3.0 28.0 + - + +
95X ASN* 4.9 0.8 + - - -
99X LYS* 3.6 37.6 + - + -
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Residues in contact with ALA 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80X LEU 2.8 21.2 + - - +
81X VAL* 3.5 1.1 - - - +
83X HIS* 1.3 71.1 - - - +
85X ASP* 1.3 65.4 + - - +
87X LEU* 2.9 9.2 + - - +
88X PHE* 2.9 23.6 + - - +
96X ALA* 4.3 0.8 - - - +
99X LYS* 3.8 21.8 - - + -
100X TYR* 3.4 44.5 - - + +
103X ALA* 5.9 0.2 - - + -
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Residues in contact with ASP 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X ALA* 5.3 4.2 - - + +
50X HIS* 3.8 19.9 + - + +
53X VAL* 6.0 0.4 - - + -
81X VAL* 3.0 30.4 + - - +
82X TYR* 3.4 25.7 - - - +
84X ALA* 1.3 74.6 - - - +
86X SER* 1.3 58.7 + - - +
88X PHE* 3.2 7.7 + - - +
89X HIS* 2.9 30.5 + - - +
100X TYR* 2.9 22.6 + - - -
141X LYS* 3.6 21.5 + - - +
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Residues in contact with SER 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X HIS* 3.5 33.2 - - - -
53X VAL* 3.8 8.5 - - - -
54X ARG* 3.7 24.1 - - - +
82X TYR 3.1 8.4 + - - -
83X HIS* 2.2 33.0 + - - -
85X ASP* 1.3 80.4 - - - +
87X LEU* 1.3 59.7 + - - +
89X HIS* 3.2 2.6 + - - +
90X ASP* 3.0 30.4 + - - +
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Residues in contact with LEU 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X ARG* 3.7 25.4 - - - +
83X HIS* 3.0 30.3 + - + +
84X ALA* 2.9 6.7 + - - +
86X SER* 1.3 73.7 - - - +
88X PHE* 1.3 56.6 + - - +
90X ASP* 3.2 8.6 + - - +
91X LYS 3.0 21.7 + - - -
92X GLU* 3.1 26.0 + - + +
95X ASN* 3.1 36.8 - - - +
96X ALA* 3.8 17.9 - - + +
99X LYS* 3.3 32.8 - - + -
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Residues in contact with PHE 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84X ALA 2.9 11.4 + - - +
85X ASP* 3.3 9.9 - - - +
87X LEU* 1.3 73.4 - - - +
89X HIS* 1.3 68.8 + - + +
91X LYS* 3.1 15.5 + - - +
92X GLU 5.0 0.9 - - - +
93X TYR* 3.7 24.7 + + - -
96X ALA* 4.0 12.0 - - + +
100X TYR* 4.3 7.6 - + - +
141X LYS* 4.4 23.8 - - + -
144X GLU* 3.6 34.5 - - + -
145X CYS* 3.4 27.4 - - - -
148X VAL* 5.5 2.2 - - + -
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Residues in contact with HIS 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X HIS* 3.4 55.8 + + + +
51X SER 5.3 0.9 - - - -
85X ASP 2.9 10.8 + - - +
86X SER 3.2 0.6 + - - +
88X PHE* 1.3 76.8 - - + +
90X ASP* 1.3 66.8 + - - +
91X LYS* 3.0 19.0 + - - +
140Y TYR* 6.1 0.9 - - - -
144Y GLU* 5.7 5.8 - - - -
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Residues in contact with ASP 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X HIS* 4.4 6.2 - - - +
51X SER* 4.5 11.5 + - - -
54X ARG* 2.6 43.3 + - - -
86X SER 3.0 15.1 + - - +
87X LEU* 3.2 11.4 + - - +
89X HIS* 1.3 84.4 - - - +
91X LYS* 1.3 71.2 - - - +
92X GLU* 3.5 18.5 + - + +
338Y HIS* 4.9 4.9 - - - -
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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
------------------------------------------------------------
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