Contacts of the helix formed by residues 57 - 73 (chain A) in PDB entry 1II7
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLU* 5.5 0.5 + - - -
55A ARG 3.6 1.2 + - - -
56A PRO* 1.3 78.1 - - - +
58A PRO* 1.4 73.8 - - - +
59A GLY* 3.3 5.3 + - - -
60A THR* 3.1 25.5 + - - -
61A LEU* 3.1 19.0 + - - +
55B ARG* 3.5 20.4 - - - +
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Residues in contact with PRO 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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56A PRO 4.5 0.4 - - - +
57A SER* 1.4 88.0 - - - +
59A GLY* 1.3 62.6 + - - +
61A LEU* 3.3 10.4 + - + +
62A LYS* 3.0 24.5 + - - +
54B SER 3.4 25.8 - - - +
55B ARG* 4.3 6.5 - - + -
56B PRO* 4.5 4.7 - - + -
61B LEU* 6.3 0.9 - - + -
88B THR* 4.9 4.3 - - + -
92B PRO* 3.5 19.3 - - + +
93B SER* 3.5 15.5 - - - +
94B VAL* 3.5 23.6 - - + +
97B LEU* 4.3 14.1 - - + +
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Residues in contact with GLY 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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57A SER* 3.1 6.0 + - - -
58A PRO* 1.3 82.0 - - - +
60A THR* 1.3 61.2 + - - +
62A LYS* 3.3 3.6 + - - +
63A LYS* 3.1 23.6 + - - +
91B GLY* 5.5 0.7 - - - -
92B PRO* 3.6 31.8 + - - +
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Residues in contact with THR 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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11A LEU* 3.8 14.7 - - + +
12A GLY* 3.6 35.7 - - - +
22A GLU* 3.9 9.8 + - - -
51A PHE* 3.8 20.0 - - + -
56A PRO* 4.0 10.9 - - + +
57A SER* 3.1 22.7 + - - -
59A GLY* 1.3 74.2 - - - +
61A LEU* 1.3 56.8 + - - +
63A LYS* 3.2 7.3 + - + +
64A ALA* 2.8 29.0 + - - +
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Residues in contact with LEU 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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51A PHE* 4.0 7.4 - - + -
56A PRO* 3.4 33.9 - - + +
57A SER 3.1 16.4 + - - +
58A PRO* 3.6 10.3 - - + +
60A THR* 1.3 78.2 - - - +
62A LYS* 1.3 57.0 + - - +
64A ALA* 3.2 3.9 + - + +
65A ILE* 2.8 40.4 + - + +
94A VAL* 3.4 22.2 - - + -
97A LEU* 4.4 10.5 - - + -
98A LEU* 5.4 5.2 - - + -
58B PRO* 6.1 1.6 - - + -
61B LEU* 3.5 31.6 - - + -
97B LEU* 4.1 18.4 - - + -
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Residues in contact with LYS 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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58A PRO 3.0 16.6 + - - +
59A GLY 3.5 4.9 - - - +
61A LEU* 1.3 76.6 - - - +
63A LYS* 1.3 57.0 + - - +
65A ILE* 3.3 6.4 + - - +
66A ALA* 2.9 29.6 + - + +
92B PRO* 3.7 31.4 - - + -
96B ASN* 5.0 7.0 - - - -
97B LEU* 4.1 16.3 - - + +
100B ASP* 2.8 36.7 + - - +
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Residues in contact with LYS 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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11A LEU* 6.1 2.2 - - + -
26A ALA* 4.2 25.3 - - + +
27A GLU* 5.0 6.1 + - - +
30A LYS* 4.9 8.9 - - - +
59A GLY 3.1 13.2 + - - +
60A THR* 3.5 10.5 - - + +
62A LYS* 1.3 74.3 - - - +
64A ALA* 1.3 66.6 + - - +
66A ALA* 3.1 9.1 + - + +
67A LEU* 2.8 58.8 + - + +
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Residues in contact with ALA 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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11A LEU* 3.6 20.8 - - + +
51A PHE* 3.4 35.7 - - + -
60A THR 2.8 18.5 + - - +
61A LEU* 3.6 4.0 - - - +
63A LYS* 1.3 72.9 - - - +
65A ILE* 1.3 58.2 + - - +
67A LEU* 3.7 3.2 - - - +
68A LEU* 2.8 39.8 + - + +
98A LEU* 4.9 6.5 - - + -
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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 LEU* 2.8 26.1 + - + +
62A LYS* 3.6 4.7 - - - +
64A ALA* 1.3 77.2 - - - +
66A ALA* 1.3 65.0 + - - +
68A LEU* 3.5 1.9 + - - +
69A GLN* 3.3 25.4 + - + +
98A LEU* 3.9 19.7 - - + -
101A PHE* 3.8 28.3 - - + -
103A LEU* 4.0 20.4 - - + +
97B LEU* 4.3 10.1 - - + -
101B PHE* 3.8 24.7 - - + -
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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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62A LYS* 2.9 17.6 + - + +
63A LYS* 3.1 8.9 + - + +
65A ILE* 1.3 79.2 - - - +
67A LEU* 1.3 66.4 + - + +
69A GLN* 3.1 22.3 + - - +
70A ILE* 3.9 5.9 + - - +
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Residues in contact with LEU 67 (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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11A LEU* 4.3 4.9 - - + -
26A ALA* 3.5 27.6 - - + +
29A PHE* 3.8 29.4 - - + -
30A LYS* 3.6 33.7 - - + -
33A LEU* 3.5 12.0 - - + +
63A LYS* 2.8 56.3 + - + +
64A ALA* 3.8 3.8 - - - +
66A ALA* 1.3 73.2 - - + +
68A LEU* 1.3 62.0 + - - +
69A GLN 3.1 1.2 + - - -
70A ILE* 3.1 27.2 + - + +
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Residues in contact with LEU 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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29A PHE* 4.2 26.9 - - + -
33A LEU* 4.9 2.9 - - + -
46A ILE* 4.7 2.9 - - + -
50A LEU* 4.5 7.2 - - + -
64A ALA* 2.8 26.8 + - + +
65A ILE 4.0 3.4 - - - +
67A LEU* 1.3 72.1 - - - +
69A GLN* 1.3 61.2 + - - +
70A ILE 3.2 0.4 - - - -
71A PRO* 3.2 18.4 - - + +
72A LYS* 3.4 10.9 + - - +
78A VAL* 4.5 22.7 - - + -
98A LEU* 3.7 31.6 - - + -
103A LEU* 4.1 36.1 - - + +
104A VAL* 3.9 15.0 - - + -
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Residues in contact with GLN 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* 3.3 18.3 + - + +
66A ALA* 3.1 17.4 + - - +
67A LEU 3.0 1.0 - - - -
68A LEU* 1.3 76.4 - - - +
70A ILE* 1.3 58.2 + - + +
72A LYS* 3.3 35.1 - - - +
73A GLU* 2.8 66.3 + - - +
103A LEU* 3.4 14.5 - - - +
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Residues in contact with ILE 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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30A LYS* 3.9 32.8 - - + +
33A LEU* 4.2 15.7 - - + +
34A GLU* 4.1 21.3 - - + +
37A VAL* 3.9 19.1 - - + -
66A ALA 4.3 4.5 - - - +
67A LEU* 3.1 22.9 + - + +
69A GLN* 1.3 79.5 - - - +
71A PRO* 1.3 71.8 - - + +
73A GLU* 3.5 5.8 + - - +
74A HIS* 3.4 23.5 - - + +
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Residues in contact with PRO 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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33A LEU* 4.3 16.8 - - + -
37A VAL* 4.2 11.7 - - + -
44A ILE* 3.8 23.3 - - + -
67A LEU 3.6 6.5 - - - +
68A LEU* 3.2 18.8 - - + +
70A ILE* 1.3 96.9 - - + +
72A LYS* 1.3 63.4 + - - +
74A HIS* 3.1 7.6 + - - -
76A ILE* 3.0 39.8 + - + +
78A VAL* 3.9 18.8 - - + -
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Residues in contact with LYS 72 (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 LEU 3.4 15.1 + - - +
69A GLN* 3.1 31.5 + - - +
71A PRO* 1.3 74.5 - - - +
73A GLU* 1.3 58.4 + - - +
74A HIS 2.9 5.6 - - - -
75A SER* 2.8 24.7 + - - +
76A ILE 4.7 4.0 - - - +
101A PHE 3.4 22.8 + - - -
102A GLY* 3.7 17.4 + - - +
103A LEU* 3.7 12.1 - - + +
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Residues in contact with GLU 73 (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 GLN* 2.8 38.3 + - - +
70A ILE* 3.6 10.1 - - - +
71A PRO 3.2 0.4 - - - -
72A LYS* 1.3 75.6 - - - +
74A HIS* 1.3 72.0 + - + +
75A SER 3.6 0.2 - - - -
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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