Contacts of the helix formed by residues 60 - 74 (chain D) in PDB entry 4LLL
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 THR 60 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C GLN* 5.7 0.7 - - - +
54D ALA* 3.7 2.9 - - - +
59D ARG* 1.3 79.0 - - - +
61D GLY* 1.3 64.3 + - - +
62D PRO* 3.2 17.1 - - - +
63D THR* 3.2 14.3 + - - -
64D VAL* 3.4 20.4 + - - +
15E C 2.8 36.4 + - - +
16E T 3.3 30.9 - - + +
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Residues in contact with GLY 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D GLN* 5.1 2.3 + - - -
51D ASN* 5.4 6.1 - - - -
54D ALA* 4.6 9.4 - - - +
60D THR* 1.3 75.5 - - - +
62D PRO* 1.3 71.5 - - - +
64D VAL* 3.5 2.6 + - - +
65D SER* 3.1 21.0 + - - -
6F G 6.2 1.1 - - - -
7F T 3.6 11.7 - - - +
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Residues in contact with PRO 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D THR* 3.2 11.9 - - - +
61D GLY* 1.3 86.0 - - - +
63D THR* 1.3 66.0 + - - +
65D SER* 2.8 15.8 + - - -
66D ASN* 2.9 14.0 + - - +
14E T 5.7 0.2 - - - -
15E C 4.7 3.8 - - - +
16E T 3.2 37.2 - - + +
17E A 3.7 8.1 - - - +
18E A 5.3 0.2 - - - +
7F T 4.0 17.9 - - + +
8F T 3.2 27.9 - - + +
9F A 4.2 2.0 - - - +
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Residues in contact with THR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ARG* 3.9 9.2 - - + -
60D THR* 3.2 12.7 + - - -
61D GLY 3.3 0.2 - - - -
62D PRO* 1.3 77.4 - - - +
64D VAL* 1.3 59.2 + - + +
66D ASN* 3.4 3.6 + - - +
67D LEU* 3.1 26.2 + - + +
13E A 4.6 2.6 - - + +
14E T 3.2 69.6 - - + +
15E C 2.4 33.3 + - - +
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D GLN* 3.9 16.2 - - + +
53D ILE* 3.7 26.5 - - + +
54D ALA* 3.6 24.2 - - + +
57D LEU* 5.3 6.1 - - + -
59D ARG* 4.4 11.9 - - + +
60D THR 3.4 18.2 + - - +
61D GLY 4.1 3.4 - - - +
62D PRO 3.1 0.4 - - - -
63D THR* 1.3 75.8 - - + +
65D SER* 1.3 67.9 + - - +
67D LEU* 4.5 8.5 - - + +
68D LEU* 3.0 39.6 + - + +
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Residues in contact with SER 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D GLN* 4.0 8.3 - - - +
61D GLY 3.1 12.6 + - - -
62D PRO* 2.8 14.3 + - - -
64D VAL* 1.3 72.5 - - - +
66D ASN* 1.3 60.2 + - - +
68D LEU* 3.9 1.5 - - - +
69D ARG* 2.9 32.4 + - - +
79D ARG* 4.3 2.8 + - - -
7F T 2.7 59.6 + - - +
8F T 4.2 3.8 + - - +
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Residues in contact with ASN 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D PRO 2.9 10.0 + - - +
63D THR 3.6 8.3 - - - +
65D SER* 1.3 76.4 + - - +
67D LEU* 1.3 65.6 + - - +
69D ARG* 3.3 43.5 + - - +
70D ASN* 3.0 31.7 + - - +
12E T 6.1 1.8 - - - +
13E A 5.6 2.6 + - - -
14E T 4.1 25.9 + - + +
15E C 6.3 0.2 - - - -
8F T 4.9 10.7 - - - +
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLU* 3.9 24.9 - - + +
33D GLN* 4.0 6.5 - - + -
36D THR* 3.1 40.6 - - + +
57D LEU* 5.3 2.2 - - + -
63D THR 3.1 13.5 + - - +
64D VAL* 4.1 8.5 - - + +
66D ASN* 1.3 78.6 - - - +
68D LEU* 1.3 65.7 + - + +
70D ASN* 3.1 5.6 + - - +
71D LEU* 3.0 30.0 + - + +
13E A 3.6 40.4 - - + +
14E T 4.2 12.8 - - - +
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D THR* 4.2 17.0 - - + -
40D LEU* 4.9 1.8 - - + -
50D GLN* 3.6 32.5 - - + -
53D ILE* 3.9 15.0 - - + -
64D VAL* 3.0 32.5 + - + +
65D SER 3.9 2.2 - - - +
67D LEU* 1.3 75.9 - - + +
69D ARG* 1.3 62.1 + - - +
71D LEU* 3.2 15.3 + - + +
72D GLU* 2.8 27.9 + - - +
77D ILE* 3.3 23.5 - - + +
79D ARG* 3.8 13.7 - - - +
91D ILE* 3.7 19.3 - - + -
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D SER* 2.9 21.6 + - - +
66D ASN* 3.4 38.0 + - - +
68D LEU* 1.3 78.6 - - - +
70D ASN* 1.3 68.1 + - - +
72D GLU* 3.5 15.8 + - - +
73D ARG* 3.0 78.3 + - + +
79D ARG* 4.4 9.3 - - - +
12E T 5.6 2.4 + - - -
8F T 4.8 15.3 + - - +
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Residues in contact with ASN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D GLN* 4.0 13.6 - - - +
66D ASN* 3.0 17.4 + - - +
67D LEU 3.1 10.5 - - - +
69D ARG* 1.3 98.3 + - - +
71D LEU* 1.3 65.4 + - - +
72D GLU 3.0 1.6 - - - -
73D ARG* 3.0 24.8 + - - +
74D LYS* 3.2 17.0 + - - +
12E T 3.6 31.8 + - - +
13E A 2.9 24.7 + - - -
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLN* 3.7 29.8 - - + +
36D THR* 4.3 8.1 - - + -
37D LEU* 3.7 42.4 - - + -
40D LEU* 5.3 0.4 - - + -
67D LEU* 3.0 34.9 + - + +
68D LEU* 3.7 15.0 - - + +
70D ASN* 1.3 78.3 - - - +
72D GLU* 1.3 59.4 + - - +
74D LYS* 3.5 7.0 + - - +
75D LYS 3.3 2.4 + - - -
76D LEU* 3.0 38.7 + - + +
77D ILE* 3.6 20.4 + - + -
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Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LEU 2.8 17.5 + - - +
69D ARG* 3.6 10.7 - - - +
70D ASN 3.0 0.2 - - - -
71D LEU* 1.3 74.7 - - - +
73D ARG* 1.3 57.9 + - - +
74D LYS 3.1 2.0 - - - -
75D LYS* 2.7 28.0 + - - +
77D ILE* 3.6 23.2 - - + +
78D TYR* 5.1 0.9 - - - -
79D ARG* 2.7 56.6 + - - +
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Residues in contact with ARG 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ARG* 3.0 72.6 + - + +
70D ASN* 3.0 16.7 + - - +
72D GLU* 1.3 77.2 - - - +
74D LYS* 1.3 57.9 + - + +
75D LYS* 3.3 9.7 + - - +
12E T 5.5 3.6 + - - -
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Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ASP* 2.7 47.3 + - + +
29D ILE* 4.0 7.3 - - - +
33D GLN* 3.4 24.9 + - - +
70D ASN 3.2 15.0 + - - +
71D LEU* 3.6 9.4 - - - +
72D GLU 3.1 0.2 - - - -
73D ARG* 1.3 75.0 - - + +
75D LYS* 1.3 65.6 + - - +
76D LEU* 3.1 25.7 + - + +
96D SER* 5.3 0.3 + - - -
12E T 5.8 2.9 - - - -
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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