Contacts of the helix formed by residues 45 - 60 (chain B) in PDB entry 1C17
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 LEU 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B PRO* 3.2 10.7 - - + -
44B ASP* 1.3 78.3 - - - +
46B ILE* 1.3 87.0 + - + +
48B LEU* 4.1 1.5 - - - +
49B LEU* 3.7 18.0 + - - +
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Residues in contact with ILE 46 (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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43B PRO* 5.5 6.7 - - + -
45B LEU* 1.3 98.5 - - + +
47B PRO* 1.3 78.4 - - + +
49B LEU* 3.1 22.4 + - + +
50B ARG* 3.1 14.6 + - + +
44C ASP* 4.2 25.6 - - + +
48C LEU* 6.2 1.1 - - + -
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Residues in contact with PRO 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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35B PHE* 3.6 2.2 - - + -
36B LEU* 6.5 0.4 - - + -
39B ALA* 3.7 39.5 - - + +
42B GLN* 4.5 11.2 - - + +
43B PRO* 2.6 29.6 - - + +
44B ASP* 4.3 2.0 - - - -
46B ILE* 1.3 98.5 - - + +
48B LEU* 1.3 52.6 + - - +
50B ARG* 4.3 7.4 - - + -
51B THR* 2.4 47.8 + - - +
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Residues in contact with LEU 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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46A ILE* 6.3 1.6 - - + -
50A ARG* 4.5 24.8 + - + +
44B ASP* 2.7 47.6 - - + +
45B LEU 4.1 2.5 - - - +
46B ILE 3.2 0.8 - - - -
47B PRO* 1.3 81.8 - - - +
49B LEU* 1.3 61.9 + - + +
51B THR* 3.8 6.9 - - - -
52B GLN* 3.2 34.4 + - + +
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Residues in contact with LEU 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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45B LEU 3.7 11.9 + - - +
46B ILE* 3.1 16.0 + - + +
48B LEU* 1.3 79.5 - - + +
50B ARG* 1.3 64.7 + - + +
52B GLN* 2.7 39.5 - - - +
53B PHE* 3.3 10.7 + - + +
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Residues in contact with ARG 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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35B PHE* 3.3 19.1 - - + -
46B ILE* 3.1 15.5 + - + +
47B PRO* 3.8 4.7 - - + +
49B LEU* 1.3 79.1 - - + +
51B THR* 1.3 66.2 + - - +
53B PHE* 3.1 36.6 + - - +
54B PHE* 3.0 46.4 + - - -
48C LEU* 4.4 26.6 + - + +
51C THR* 3.9 15.4 - - - +
52C GLN* 4.2 12.5 - - - +
55C ILE* 3.2 28.2 - - - +
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Residues in contact with THR 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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35A PHE* 5.9 0.9 - - + -
50A ARG* 3.9 18.6 - - - +
54A PHE* 4.4 14.4 - - + -
32B GLY* 4.9 7.6 - - - +
35B PHE* 3.0 28.7 - - + -
36B LEU* 5.1 15.9 - - + +
39B ALA* 5.7 0.2 - - - +
47B PRO* 2.4 33.5 + - - +
48B LEU* 3.8 7.3 - - - -
50B ARG* 1.3 73.2 - - - +
52B GLN* 1.3 63.8 + - - +
54B PHE* 3.1 4.5 + - - +
55B ILE* 3.0 26.8 + - + +
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Residues in contact with GLN 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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50A ARG* 4.3 8.1 - - - +
53A PHE* 6.4 1.1 - - + -
48B LEU* 3.2 21.1 + - + +
49B LEU* 2.7 48.4 - - - +
51B THR* 1.3 75.9 - - - +
53B PHE* 1.3 60.7 + - - +
55B ILE* 3.4 12.6 - - + -
56B VAL* 2.7 51.1 + - + +
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Residues in contact with PHE 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 LEU* 3.7 13.0 - - + +
50B ARG* 3.1 44.4 + - - +
52B GLN* 1.3 82.5 - - - +
54B PHE* 1.3 57.8 + + - +
56B VAL* 4.2 4.0 - - + +
57B MET* 2.9 51.6 + - + +
52C GLN* 6.4 1.6 - - + -
55C ILE* 5.4 2.5 - - + -
56C VAL* 6.4 1.6 - - + -
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Residues in contact with PHE 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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28B ILE* 5.3 0.4 - - - -
31B LEU* 3.0 49.0 - - + +
32B GLY* 5.2 0.2 - - - -
35B PHE* 3.3 39.9 - + + -
50B ARG* 3.0 44.8 + - - -
51B THR* 3.1 7.2 + - - +
52B GLN 3.0 1.4 + - - -
53B PHE* 1.3 74.3 - + - +
55B ILE* 1.3 59.2 - - + +
56B VAL 2.9 1.1 - - - -
57B MET* 2.6 31.7 + - + +
58B GLY* 2.9 10.0 + - - -
32C GLY 5.2 2.7 - - - -
36C LEU* 6.3 0.2 - - + -
51C THR* 4.3 7.0 - - + -
55C ILE* 3.2 50.3 - - + -
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Residues in contact with ILE 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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50A ARG* 3.1 33.0 - - - +
53A PHE* 5.4 3.4 - - + -
54A PHE* 3.3 33.7 - - + -
57A MET* 4.5 15.2 - - + +
28B ILE* 3.2 32.2 - - + +
32B GLY* 3.4 28.5 - - - -
51B THR* 3.0 10.5 + - + +
52B GLN* 3.2 16.6 - - + +
54B PHE* 1.3 76.7 - - - +
56B VAL* 1.3 63.9 + - + +
58B GLY 3.8 0.2 - - - -
59B LEU* 2.9 23.3 + - - +
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Residues in contact with VAL 56 (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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53A PHE* 6.4 1.6 - - + -
57A MET* 5.7 3.4 - - + -
52B GLN* 2.7 46.3 + - + +
53B PHE* 4.2 3.8 - - + +
54B PHE 2.8 0.2 + - - -
55B ILE* 1.3 77.3 - - + +
57B MET* 1.3 51.3 + - - +
58B GLY 2.8 4.7 - - - -
59B LEU* 2.6 35.9 + - + -
60B VAL* 2.7 37.0 + - + +
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Residues in contact with MET 57 (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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31B LEU* 5.0 2.2 - - + -
53B PHE* 2.9 59.6 + - + +
54B PHE* 2.6 21.9 + - + +
56B VAL* 1.3 72.1 - - - +
58B GLY* 1.3 55.4 + - - +
60B VAL* 3.6 9.3 + - - +
61B ASP* 3.4 18.4 + - - +
28C ILE* 4.2 26.2 - - + -
55C ILE* 4.4 20.6 - - + +
56C VAL* 5.7 3.6 - - + -
59C LEU* 4.0 40.3 - - + +
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Residues in contact with GLY 58 (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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24B ALA* 3.0 34.3 - - - +
27B GLY* 5.2 2.0 - - - -
28B ILE* 3.0 25.4 - - - +
31B LEU* 6.1 1.3 - - - +
54B PHE 2.9 9.4 + - - -
56B VAL 2.8 0.8 - - - -
57B MET* 1.3 76.0 - - - +
59B LEU* 1.3 55.3 + - - +
60B VAL 3.0 4.9 - - - -
61B ASP* 3.1 10.9 + - - -
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Residues in contact with LEU 59 (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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57A MET* 4.1 36.6 - - + +
61A ASP* 5.5 8.3 - - + +
24B ALA* 5.3 0.2 - - - -
28B ILE* 2.9 13.2 - - + +
55B ILE 2.9 15.3 + - - +
56B VAL* 2.6 26.1 + - + +
58B GLY* 1.3 72.0 - - - +
60B VAL* 1.3 58.4 + - + +
61B ASP 3.5 0.2 - - - -
62B ALA* 4.6 5.9 + - + +
63B ILE* 3.7 20.4 + - + +
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Residues in contact with VAL 60 (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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56B VAL* 2.7 34.7 + - + +
57B MET* 3.9 8.7 - - - +
58B GLY 3.0 0.2 - - - -
59B LEU* 1.3 83.1 - - + +
61B ASP* 1.3 52.6 + - - +
62B ALA 3.3 2.2 - - - -
63B ILE* 4.2 16.6 - - + -
64B PRO* 2.7 35.5 - - + +
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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