Contacts of the helix formed by residues 52 - 65 (chain A) in PDB entry 3LC4
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 ASN 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLU* 2.8 24.5 + - - +
50A LEU 3.0 0.4 - - - -
51A LYS* 1.3 84.8 - - + +
53A ILE* 1.3 58.9 + - - +
54A PRO* 3.1 10.2 - - - +
55A LYS* 2.6 44.9 + - + +
56A SER* 3.3 13.5 + - - -
476A ILE* 3.3 32.8 - - + +
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Residues in contact with ILE 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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48A LEU* 4.0 28.3 - - + -
49A GLU 3.1 22.6 + - - +
50A LEU* 3.9 21.4 + - + +
52A ASN* 1.3 69.6 - - - +
54A PRO* 1.4 66.8 - - + +
56A SER* 2.6 28.4 + - - -
57A PHE* 2.8 48.9 + - + -
216A GLN* 4.4 22.9 - - + +
366A SER* 4.8 2.0 - - - +
476A ILE 4.2 2.5 + - - +
477A GLY* 5.9 1.3 - - - -
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Residues in contact with PRO 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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52A ASN* 3.3 8.3 - - - +
53A ILE* 1.4 92.5 - - + +
55A LYS* 1.3 55.4 + - - +
57A PHE* 3.1 16.3 + - + +
58A THR* 2.9 31.5 + - - -
81A HIS* 4.8 0.5 + - - -
365A PRO* 4.0 15.5 - - + -
366A SER* 3.7 17.5 - - - +
394A ASP* 3.3 27.1 - - - +
476A ILE* 3.7 28.7 - - + +
477A GLY 5.1 3.1 - - - +
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Residues in contact with LYS 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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49A GLU* 4.3 19.3 + - - +
52A ASN* 2.6 39.3 + - + +
54A PRO* 1.3 70.4 - - - +
56A SER* 1.3 59.5 + - - +
58A THR* 3.4 11.2 + - + +
59A ARG* 2.9 28.4 + - - +
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Residues in contact with SER 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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47A GLN 3.8 17.7 + - - -
48A LEU* 3.7 10.9 - - - -
49A GLU* 2.8 32.9 + - - +
52A ASN 3.3 7.4 + - - -
53A ILE* 2.6 19.5 + - - -
55A LYS* 1.3 71.8 - - - +
57A PHE* 1.3 57.9 + - - -
59A ARG* 2.9 9.1 + - - +
60A LEU* 2.8 36.7 + - - +
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Residues in contact with PHE 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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48A LEU* 4.7 7.9 - - + -
53A ILE* 2.8 37.5 + - + -
54A PRO* 3.2 11.4 - - + +
56A SER* 1.3 76.1 - - - +
58A THR* 1.3 53.8 + - - +
59A ARG 3.1 0.3 + - - -
60A LEU* 3.2 2.1 + - + +
61A ALA* 2.7 35.4 + - - +
68A PHE* 3.6 22.1 - + + -
70A LEU* 3.8 24.5 - - + -
77A MET* 4.8 12.3 - - - -
79A VAL* 3.9 17.0 - - + -
81A HIS* 4.3 11.7 - - + -
366A SER* 3.8 18.6 - - - -
390A VAL* 4.0 19.3 - - + -
392A THR* 3.8 16.4 - - + -
394A ASP* 6.1 0.9 - - - +
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Residues in contact with THR 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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54A PRO 2.9 16.3 + - - -
55A LYS* 3.5 14.9 - - + +
57A PHE* 1.3 74.0 - - - +
59A ARG* 1.3 62.9 + - - +
61A ALA* 3.2 13.3 + - - +
62A GLN* 3.4 28.6 + - - +
81A HIS* 2.9 32.1 + - + -
394A ASP* 4.5 6.2 + - - -
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Residues in contact with ARG 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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46A PHE 5.1 0.4 + - - -
47A GLN* 2.9 50.5 + - - +
55A LYS* 2.9 14.2 + - + +
56A SER* 2.9 10.5 + - - +
58A THR* 1.3 77.2 - - - +
60A LEU* 1.3 68.8 + - - +
62A GLN* 3.3 26.4 + - - +
63A ARG* 2.5 44.2 + - - +
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Residues in contact with LEU 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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36A PRO* 3.9 16.2 - - + -
47A GLN* 3.3 25.8 - - + +
48A LEU* 4.0 13.2 - - + -
56A SER 2.8 33.1 + - - +
57A PHE* 3.6 5.4 - - - +
59A ARG* 1.3 78.6 - - - +
61A ALA* 1.3 65.1 + - - +
62A GLN 3.1 2.0 - - - -
63A ARG* 3.0 37.2 + - - +
64A PHE* 3.1 34.4 + - + +
68A PHE* 3.6 25.0 - - + -
70A LEU* 4.5 6.1 - - + -
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Residues in contact with ALA 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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57A PHE 2.7 15.4 + - - +
58A THR 3.2 10.1 + - - +
60A LEU* 1.3 72.0 - - - +
62A GLN* 1.3 58.3 + - + +
63A ARG 3.2 0.2 - - - -
65A GLY* 2.6 45.8 + - - +
68A PHE* 3.6 4.9 - - + -
81A HIS* 3.2 41.5 - - + +
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Residues in contact with GLN 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 THR* 3.5 32.9 + - - +
59A ARG* 3.3 14.8 + - - +
60A LEU 3.1 1.2 - - - -
61A ALA* 1.3 78.4 - - + +
63A ARG* 1.3 59.4 + - - +
65A GLY 4.6 1.1 - - - -
81A HIS* 5.9 0.4 - - - -
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Residues in contact with ARG 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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36A PRO* 4.6 5.3 - - - +
47A GLN* 3.4 17.2 + - - -
59A ARG* 2.5 49.0 + - - +
60A LEU* 3.0 19.7 + - - +
62A GLN* 1.3 79.8 - - - +
64A PHE* 1.3 100.2 + - + +
65A GLY 3.7 0.7 - - - -
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Residues in contact with PHE 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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34A PRO* 4.1 19.9 - - + +
35A GLY* 3.5 34.3 - - - -
36A PRO* 3.6 20.0 - - + -
60A LEU* 3.1 48.8 + - + +
63A ARG* 1.3 121.6 - - + +
65A GLY* 1.3 61.4 + - - +
66A PRO* 4.3 1.2 - - - +
67A VAL 3.6 11.1 - - - +
68A PHE* 3.9 18.6 - - + -
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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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61A ALA* 2.6 42.0 + - - +
62A GLN 4.6 0.6 - - - -
63A ARG 3.7 0.4 - - - -
64A PHE* 1.3 77.3 - - - +
66A PRO* 1.3 74.1 - - - +
67A VAL 3.5 0.7 + - - -
68A PHE* 3.7 6.8 - - - -
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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