Contacts of the helix formed by residues 45 - 60 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A PRO* 3.2 10.7 - - + -
44A ASP* 1.3 79.1 - - - +
46A ILE* 1.3 86.0 + - + +
48A LEU* 4.1 1.2 - - - +
49A LEU* 3.7 17.7 + - - +
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Residues in contact with ILE 46 (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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43A PRO* 5.5 6.7 - - + -
45A LEU* 1.3 99.2 - - + +
47A PRO* 1.3 78.2 - - + +
49A LEU* 3.1 23.3 + - + +
50A ARG* 3.1 14.0 + - + +
44B ASP* 4.3 23.8 - - + +
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Residues in contact with PRO 47 (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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35A PHE* 3.6 2.6 - - + -
36A LEU* 6.5 0.2 - - + -
39A ALA* 3.7 39.5 - - + +
42A GLN* 4.5 11.9 - - + +
43A PRO* 2.6 28.7 - - + +
44A ASP* 4.3 1.6 - - - -
46A ILE* 1.3 98.5 - - + +
48A LEU* 1.3 54.1 + - - +
50A ARG* 4.3 8.1 - - + -
51A THR* 2.4 48.2 + - - +
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Residues in contact with LEU 48 (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* 2.7 47.8 - - + +
45A LEU 4.1 2.0 - - - +
46A ILE 3.2 0.4 - - - -
47A PRO* 1.3 81.1 - - - +
49A LEU* 1.3 62.9 + - + +
51A THR* 3.8 6.9 - - - -
52A GLN* 3.2 34.9 + - + +
42L GLN* 5.0 9.6 - - - +
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Residues in contact with LEU 49 (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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45A LEU 3.7 11.1 + - - +
46A ILE* 3.1 16.7 + - + +
48A LEU* 1.3 79.1 - - + +
50A ARG* 1.3 64.9 + - + +
52A GLN* 2.7 39.1 - - - +
53A PHE* 3.3 10.8 + - + +
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Residues in contact with ARG 50 (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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35A PHE* 3.3 19.0 - - + -
46A ILE* 3.1 15.8 + - + +
47A PRO* 3.8 4.5 - - + +
49A LEU* 1.3 77.4 - - + +
51A THR* 1.3 65.3 + - - +
53A PHE* 3.1 34.8 + - - +
54A PHE* 3.0 46.7 + - - -
48B LEU* 4.5 24.3 + - + +
51B THR* 3.9 15.4 - - - +
52B GLN* 4.3 11.7 - - - +
55B ILE* 3.1 28.9 - - - +
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Residues in contact with THR 51 (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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32A GLY 4.9 7.6 - - - +
35A PHE* 3.0 28.4 - - + -
36A LEU* 5.1 15.9 - - + +
39A ALA* 5.7 0.3 - - - +
47A PRO* 2.4 33.6 + - - +
48A LEU* 3.8 8.2 - - - +
50A ARG* 1.3 73.4 - - - +
52A GLN* 1.3 61.7 + - - +
54A PHE* 3.1 4.3 + - - +
55A ILE* 3.0 41.6 + - + +
34L LYS* 5.8 3.4 - - + -
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Residues in contact with GLN 52 (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 LEU* 3.2 23.0 + - + +
49A LEU* 2.7 47.2 - - - +
51A THR* 1.3 75.6 - - - +
53A PHE* 1.3 62.7 + - + +
55A ILE* 3.4 15.9 - - + -
56A VAL* 2.7 51.0 + - + +
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Residues in contact with PHE 53 (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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49A LEU* 3.7 13.2 - - + +
50A ARG* 3.1 44.4 + - - +
52A GLN* 1.3 83.0 - - + +
54A PHE* 1.3 57.2 + + - +
56A VAL* 4.2 4.4 - - + +
57A MET* 2.9 51.2 + - + +
52B GLN* 6.4 1.6 - - + -
55B ILE* 5.4 1.8 - - + -
56B VAL* 6.4 1.3 - - + -
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Residues in contact with PHE 54 (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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28A ILE* 5.3 0.4 - - - -
31A LEU* 3.0 51.2 - - + +
35A PHE* 3.3 39.0 - + + -
50A ARG* 3.0 44.2 + - - -
51A THR* 3.1 7.0 + - - +
52A GLN 3.0 1.6 + - - -
53A PHE* 1.3 75.3 - + + +
55A ILE* 1.3 60.6 + - + +
56A VAL 2.9 0.9 - - - -
57A MET* 2.6 33.0 + - + +
58A GLY* 2.9 9.5 + - - -
32B GLY 5.2 2.9 - - - -
36B LEU* 6.4 0.2 - - + -
51B THR* 4.4 6.1 - - + -
55B ILE* 3.3 48.7 - - + -
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Residues in contact with ILE 55 (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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28A ILE* 3.2 30.0 - - + +
32A GLY* 3.4 29.6 - - - -
51A THR* 3.0 20.1 + - + +
52A GLN* 3.2 26.2 - - + +
54A PHE* 1.3 76.4 - - - +
56A VAL* 1.3 64.0 + - + +
59A LEU* 2.9 23.3 + - - +
31L LEU* 3.5 28.0 - - + -
34L LYS* 3.5 18.8 - - + +
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Residues in contact with VAL 56 (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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52A GLN* 2.7 45.6 + - + +
53A PHE* 4.2 4.9 - - + +
54A PHE 2.8 0.2 + - - -
55A ILE* 1.3 77.1 - - + +
57A MET* 1.3 51.7 + - - +
58A GLY 2.8 4.5 - - - -
59A LEU* 2.6 36.5 + - + -
60A VAL* 2.7 37.3 + - + +
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Residues in contact with MET 57 (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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31A LEU* 5.0 2.7 - - + -
53A PHE* 2.9 61.0 + - + +
54A PHE* 2.6 22.8 + - + +
56A VAL* 1.3 72.2 - - - +
58A GLY* 1.3 56.6 + - - -
60A VAL* 3.6 8.9 + - - +
61A ASP* 3.4 18.0 + - - +
28B ILE* 4.2 26.7 - - + -
55B ILE* 4.5 17.7 - - + +
56B VAL* 5.7 3.1 - - + -
59B LEU* 4.1 39.8 - - + +
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Residues in contact with GLY 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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24A ALA* 3.0 35.1 - - - +
27A GLY* 5.2 1.3 - - - -
28A ILE* 3.0 25.5 - - - +
31A LEU* 6.1 1.3 - - - +
54A PHE 2.9 8.8 + - - -
56A VAL 2.8 1.0 - - - -
57A MET* 1.3 76.2 - - - +
59A LEU* 1.3 54.5 + - - +
60A VAL 3.0 5.2 - - - -
61A ASP* 3.1 10.7 + - - -
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Residues in contact with LEU 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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24A ALA* 5.3 0.2 - - - -
28A ILE* 2.9 15.2 - - + +
55A ILE 2.9 14.7 + - - +
56A VAL* 2.6 28.0 + - + +
58A GLY* 1.3 72.6 - - - +
60A VAL* 1.3 58.8 + - + +
61A ASP 3.5 0.4 - - - -
62A ALA* 4.6 5.3 + - + +
63A ILE* 3.7 19.6 + - + +
31L LEU* 5.7 9.2 - - + -
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Residues in contact with VAL 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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56A VAL* 2.7 35.2 + - + +
57A MET* 3.9 9.0 - - - +
58A GLY 3.0 0.2 - - - -
59A LEU* 1.3 82.6 - - + +
61A ASP* 1.3 51.2 + - - +
62A ALA 3.3 2.2 - - - -
63A ILE* 4.0 16.6 - - + -
64A PRO* 2.7 32.2 - - + +
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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