Contacts of the helix formed by residues 63 - 75 (chain A) in PDB entry 1I4S
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 ARG 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ASN* 2.8 23.8 + - - +
62A LYS* 1.3 82.3 - - - +
64A GLU* 1.3 66.3 + - - +
65A GLY* 4.1 6.5 - - - +
66A PHE* 2.9 7.7 + - - +
67A LEU* 2.9 23.4 + - - +
237B GLU* 3.4 9.2 - - - +
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Residues in contact with GLU 64 (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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62A LYS 3.9 0.8 + - - -
63A ARG* 1.3 72.0 - - - +
65A GLY* 1.3 64.5 + - - +
67A LEU* 4.0 12.7 - - - +
68A SER* 2.9 48.8 + - - -
237B GLU* 2.8 29.6 + - + +
238B THR* 6.3 0.2 - - - +
241B PHE* 4.5 14.3 - - + -
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Residues in contact with GLY 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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63A ARG* 3.0 6.0 - - - +
64A GLU* 1.3 89.8 - - - +
66A PHE* 1.3 55.4 + - - +
69A PRO* 3.3 21.8 - - - +
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Residues in contact with PHE 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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59A SER* 3.3 27.1 - - - -
60A PRO* 3.8 25.4 - - + -
61A ASN* 3.0 43.7 - - + +
63A ARG* 2.9 5.1 + - + +
65A GLY* 1.3 76.0 - - - +
67A LEU* 1.3 66.9 + - - +
69A PRO* 3.7 9.0 - - - +
70A LEU* 3.5 37.2 - - + +
143A ILE 5.3 1.1 - - - -
146A GLY* 5.1 9.9 - - - -
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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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55A LEU* 3.6 24.6 - - + +
56A VAL* 4.4 5.6 - - + -
59A SER* 3.6 15.3 - - - +
61A ASN 3.5 20.9 - - - +
62A LYS* 3.8 14.8 - - - +
63A ARG 2.9 31.8 + - - +
64A GLU 3.9 2.7 - - - +
66A PHE* 1.3 76.6 - - - +
68A SER* 1.3 54.7 + - - +
70A LEU* 3.1 5.4 + - - +
71A LYS* 2.5 36.6 + - - +
238B THR* 4.3 13.0 - - + -
241B PHE* 3.3 42.2 - - + -
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Residues in contact with SER 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 GLU* 2.9 40.5 + - - -
67A LEU* 1.3 76.1 - - - +
69A PRO* 1.3 63.7 - - - +
71A LYS* 3.2 7.0 + - - +
72A ALA* 2.7 28.8 + - - +
241B PHE* 3.3 18.4 - - - -
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Residues in contact with PRO 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 GLY* 3.3 26.0 - - - +
66A PHE* 3.7 7.2 - - - +
67A LEU 3.6 2.0 - - - -
68A SER* 1.3 96.3 - - - +
70A LEU* 1.3 56.7 + - - +
72A ALA* 3.1 11.2 - - + +
73A TYR* 3.0 25.8 + - - +
147A ARG* 5.0 3.3 - - - +
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Residues in contact with LEU 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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55A LEU* 4.3 15.9 - - + -
66A PHE* 3.5 41.7 - - + +
67A LEU* 3.1 9.1 + - - +
69A PRO* 1.3 76.4 - - - +
71A LYS* 1.3 68.3 + - - +
73A TYR* 3.1 11.4 + - + +
74A LEU* 2.9 46.5 + - + +
142A ALA 4.6 5.8 - - - +
143A ILE* 4.4 27.8 - - + +
146A GLY* 4.6 16.6 - - - +
147A ARG* 4.9 4.9 - - - +
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Residues in contact with LYS 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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48A ASN* 3.4 22.7 - - - +
51A ILE* 5.1 4.0 - - + -
52A VAL* 3.7 24.9 - - + -
55A LEU* 4.5 8.4 - - + +
67A LEU 2.5 20.8 + - - +
68A SER* 3.3 6.7 + - - +
70A LEU* 1.3 72.3 - - - +
72A ALA* 1.3 64.4 + - - +
74A LEU* 3.0 17.7 + - - +
75A ILE* 3.1 45.9 + - + +
241B PHE* 3.8 23.1 - - + +
244B ASP* 5.8 4.3 - - - -
245B ALA* 5.9 0.4 - - - -
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Residues in contact with ALA 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 SER 2.7 16.7 + - - +
69A PRO* 3.1 18.4 - - + +
71A LYS* 1.3 78.3 - - - +
73A TYR* 1.3 60.0 + - - +
75A ILE* 3.8 8.8 + - - +
76A SER* 3.6 17.3 + - - -
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Residues in contact with TYR 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 PRO 3.0 10.5 + - - +
70A LEU* 3.1 8.9 + - + +
72A ALA* 1.3 78.3 - - - +
74A LEU* 1.3 69.0 + - + +
75A ILE 3.1 0.7 - - - -
76A SER* 2.9 39.7 + - - -
78A GLU* 4.9 7.9 - - + -
79A PHE* 3.4 41.6 + + + +
82A LEU* 5.4 4.0 - - - +
142A ALA* 3.9 19.6 - - + +
145A GLU* 5.5 3.5 + - - -
147A ARG* 3.9 34.3 - - - +
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Residues in contact with LEU 74 (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 ILE* 3.9 22.2 - - + +
55A LEU* 4.0 22.7 - - + -
70A LEU* 2.9 37.8 + - + +
71A LYS 3.0 4.8 + - - +
73A TYR* 1.3 79.4 - - + +
75A ILE* 1.3 59.8 + - - +
76A SER 3.5 0.2 - - - -
79A PHE* 3.2 43.8 - - + -
80A PHE* 3.7 8.5 - - - -
139A ILE* 4.1 18.8 - - + +
142A ALA* 3.8 27.1 - - + -
143A ILE* 4.1 9.9 - - + -
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Residues in contact with ILE 75 (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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44A ASP* 5.5 7.0 - - - +
48A ASN* 4.1 27.8 - - + +
51A ILE* 3.9 24.7 - - + -
71A LYS* 3.1 43.0 + - + +
72A ALA* 3.9 8.5 - - - +
73A TYR 3.1 0.6 - - - -
74A LEU* 1.3 82.3 - - - +
76A SER* 1.3 66.0 + - - +
80A PHE* 3.8 24.5 - - + -
110A GLU* 5.1 0.9 - - - +
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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
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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