Contacts of the helix formed by residues 46 - 55 (chain B) in PDB entry 1CI1
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 PHE 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.5 37.2 - + + -
47A LEU* 3.7 14.4 - - + +
77A GLY* 3.6 26.5 - - - -
79A VAL* 4.7 4.2 - - + +
44B PRO 3.6 1.2 + - - -
45B THR* 1.3 73.1 - - - +
47B LEU* 1.3 62.6 + - - +
49B ILE* 3.2 33.1 + - + +
50B PRO* 3.4 9.0 - - - +
65B ALA* 4.1 13.0 - - + -
66B GLN* 4.9 3.4 - - + -
67B ASN* 3.1 41.1 - - + -
68B ALA* 4.7 1.1 - - - -
78B GLU* 5.8 1.8 - - - -
79B VAL* 3.9 39.7 - - + -
84B LEU* 4.4 4.5 - - + -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.7 26.5 - - + +
49A ILE* 3.8 33.9 - - + -
50A PRO* 3.5 16.1 - - + +
79A VAL* 4.8 8.4 - - + +
83A ILE* 3.6 29.6 - - + +
84A LEU* 4.4 14.6 - - + -
87A TYR* 4.0 36.3 - - + -
45B THR* 3.1 9.3 + - - +
46B PHE* 1.3 80.1 - - - +
48B HIS* 1.3 62.9 + - + +
50B PRO* 3.5 11.3 - - - +
51B MET* 5.1 1.7 + - - +
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Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 3.5 33.0 + - + +
86A ASP* 5.7 0.2 + - - -
87A TYR* 5.0 10.9 - + - +
13B TRP* 6.0 0.2 - - - -
16B ASN 4.1 8.5 + - - -
17B GLY* 3.6 24.8 - - - -
18B SER* 4.1 11.7 + - - -
19B GLU 5.0 0.9 + - - -
22B LEU* 3.6 27.3 - - + +
44B PRO* 4.1 9.4 - - + +
45B THR* 3.0 23.6 + - - +
47B LEU* 1.3 86.0 - - + +
49B ILE* 1.3 63.0 + - - +
50B PRO* 3.3 3.4 - - - -
51B MET* 3.3 18.5 - - + +
52B THR* 2.9 28.3 + - - +
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.5 16.4 - - + -
44B PRO* 4.2 19.7 - - + +
45B THR 3.2 9.5 + - - +
46B PHE* 3.2 22.5 + - + +
48B HIS* 1.3 77.4 - - - +
50B PRO* 1.3 63.5 - - + +
52B THR* 3.2 6.9 + - - -
53B LYS* 2.9 28.7 + - + +
63B ILE* 4.2 6.5 - - + +
64B ALA 4.3 13.2 - - - +
65B ALA* 4.4 8.7 - - - -
84B LEU* 4.2 23.1 - - + -
87B TYR* 4.0 8.1 - - + -
89B ILE* 3.7 27.8 - - + -
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Residues in contact with PRO 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.6 16.8 - - + +
50A PRO* 3.5 33.4 - - + -
46B PHE 3.4 10.3 - - - +
47B LEU 3.5 5.6 - - - +
48B HIS 3.4 3.6 - - - -
49B ILE* 1.3 96.2 - - + +
51B MET* 1.3 61.6 + - - +
53B LYS* 3.4 2.3 + - - +
54B ALA* 3.2 23.7 + - - +
87B TYR* 3.0 33.0 + - + +
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Residues in contact with MET 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PRO* 5.8 0.4 - - - +
87A TYR* 6.0 9.0 - - + +
19B GLU* 3.9 25.8 - - + -
22B LEU* 4.4 19.3 - - + -
23B VAL* 3.3 42.4 - - + +
26B ILE* 4.6 3.8 - - + -
47B LEU 5.1 1.1 + - - +
48B HIS* 3.3 25.0 + - + +
49B ILE 3.4 0.2 - - - -
50B PRO* 1.3 79.7 - - - +
52B THR* 1.3 68.4 + - - +
54B ALA* 3.6 4.8 + - - +
55B ARG* 3.3 53.1 + - - +
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Residues in contact with THR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TRP* 4.1 10.3 - - + -
22B LEU* 5.1 0.9 - - - +
26B ILE* 3.9 24.0 - - + +
42B VAL* 4.3 7.9 - - + -
44B PRO* 3.8 26.2 - - + +
48B HIS* 2.9 17.3 + - - +
49B ILE* 3.2 4.7 + - - -
51B MET* 1.3 80.5 - - - +
53B LYS* 1.3 58.9 + - - +
56B LEU* 2.9 51.4 + - + +
63B ILE* 4.3 12.1 - - + -
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 2.9 16.6 + - + +
50B PRO* 3.4 6.5 + - + +
52B THR* 1.3 77.3 - - - +
54B ALA* 1.3 60.9 + - - +
55B ARG 3.6 0.3 + - - -
56B LEU 4.3 9.0 + - - +
63B ILE* 3.5 21.5 - - + +
87B TYR* 3.4 45.1 + - + +
88B GLY* 4.5 11.2 + - - +
89B ILE* 4.2 15.3 - - + -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PRO 3.2 16.9 + - - +
51B MET* 4.0 7.2 - - - +
52B THR 3.2 0.6 - - - -
53B LYS* 1.3 78.6 - - - +
55B ARG* 1.3 64.0 + - + +
56B LEU 5.4 0.2 - - - -
57B THR* 5.9 0.7 - - - +
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU* 4.2 13.1 + - - -
23B VAL* 3.7 31.3 - - - +
26B ILE* 4.0 17.7 - - + -
30B ASN* 2.8 28.9 + - - +
51B MET* 3.3 44.7 + - - +
52B THR 3.4 1.4 + - - -
53B LYS 3.3 0.2 - - - -
54B ALA* 1.3 87.9 - - + +
56B LEU* 1.3 57.6 + - - +
57B THR* 3.3 9.2 + - - +
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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