Contacts of the helix formed by residues 58 - 76 (chain B) in PDB entry 3LDZ
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 ASP 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU* 3.5 33.0 - - - +
56B HIS* 3.1 24.0 - - + +
57B LYS* 1.4 76.6 - - + +
59B PRO* 1.4 72.2 - - - +
60B HIS* 3.2 25.9 + - - +
61B VAL* 3.1 15.4 + - + +
62B ALA* 3.2 11.8 + - - +
59C PRO* 5.7 3.1 - - - +
101C HIS* 6.0 0.7 - - - -
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Residues in contact with PRO 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B HIS 5.3 0.2 - - - +
57B LYS 3.4 10.8 - - - +
58B ASP* 1.4 89.5 - - - +
60B HIS* 1.3 54.6 + - - +
61B VAL 3.2 0.2 - - - -
62B ALA* 3.7 9.1 - - + +
63B MET* 2.9 39.1 + - + +
101B HIS* 3.8 47.3 - - + +
103B LYS* 5.7 3.6 - - + -
104B VAL* 4.2 4.9 - - + -
58C ASP* 6.5 2.2 - - - -
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 3.1 35.9 + - + -
21B ASN 2.7 29.3 + - - -
22B THR 5.0 2.2 - - - -
58B ASP* 3.2 15.3 + - - +
59B PRO* 1.3 77.0 - - - +
61B VAL* 1.4 58.6 + - - +
63B MET* 4.0 5.5 + - - +
64B GLN* 3.1 52.0 + - + +
59C PRO* 5.0 16.9 - - + +
101C HIS* 3.4 13.2 + + - -
103C LYS* 4.0 20.4 + - - -
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.4 28.3 - - - +
19B GLU* 3.7 33.0 - - + +
53B ARG* 3.6 28.7 - - - +
56B HIS* 3.6 31.0 - - + +
58B ASP* 3.1 20.3 + - + +
60B HIS* 1.4 73.1 - - - +
62B ALA* 1.3 59.8 + - - +
64B GLN* 3.1 7.2 + - - +
65B ALA* 3.0 25.3 + - - +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ARG 3.5 13.7 - - - +
54B VAL* 3.7 21.9 - - - +
56B HIS* 4.2 8.5 - - - +
58B ASP 3.2 9.4 + - - +
59B PRO* 3.7 4.9 - - + +
61B VAL* 1.3 79.5 - - - +
63B MET* 1.4 55.9 + - - +
65B ALA* 3.4 4.4 - - - +
66B LEU* 3.2 32.1 + - - +
104B VAL* 3.7 23.6 - - + -
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Residues in contact with MET 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PRO* 2.9 27.4 + - + +
60B HIS* 4.1 6.5 - - - +
62B ALA* 1.4 72.8 - - - +
64B GLN* 1.3 65.4 + - + +
65B ALA 3.2 0.2 - - - -
66B LEU* 3.1 8.0 + - - +
67B THR* 3.1 24.4 + - - -
103B LYS* 3.5 65.5 - - + +
104B VAL* 3.9 12.8 - - + -
107B LYS* 4.1 22.7 - - + +
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA 3.4 13.9 + - - +
17B THR* 3.7 17.9 - - - +
18B SER 2.8 20.9 + - - +
21B ASN* 3.1 37.3 - - - +
23B ALA 5.0 4.4 + - - -
24B GLU* 5.6 12.7 - - + +
29B ILE* 5.7 1.9 - - - +
60B HIS* 3.1 36.3 + - + +
61B VAL 3.1 8.4 + - - +
63B MET* 1.3 79.7 - - + +
65B ALA* 1.3 59.8 + - - +
67B THR* 3.5 10.2 + - - +
68B LEU* 3.2 21.1 + - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.5 10.7 - - + +
50B ILE* 3.4 16.8 - - + +
53B ARG* 3.8 15.0 - - + -
54B VAL* 3.7 31.2 - - + +
61B VAL 3.0 12.2 + - - +
62B ALA 3.4 10.5 - - - +
64B GLN* 1.3 76.9 - - - +
66B LEU* 1.3 57.1 + - - +
68B LEU* 3.3 4.0 + - - +
69B LEU* 2.9 22.9 + - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.8 20.6 - - + -
62B ALA 3.2 16.6 + - - +
63B MET* 3.1 11.4 + - - +
65B ALA* 1.3 74.4 - - - +
67B THR* 1.3 58.0 + - - +
69B LEU* 3.5 24.2 - - + +
70B GLY* 2.9 26.0 + - - -
104B VAL* 3.5 41.5 - - + +
107B LYS* 3.7 28.3 - - + -
108B LEU* 3.9 19.1 - - + +
111B LEU* 3.7 16.0 - - + +
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.9 27.2 + - + +
26B TRP* 3.6 31.9 - - + -
29B ILE* 4.6 7.6 - - + -
63B MET 3.1 12.4 + - - -
64B GLN* 3.8 10.5 - - - +
65B ALA 3.4 0.4 - - - -
66B LEU* 1.3 75.9 - - - +
68B LEU* 1.4 57.1 + - - +
70B GLY* 3.6 2.3 + - - -
71B ALA* 3.0 27.7 + - - +
107B LYS* 4.4 14.9 + - - +
47E GLY* 5.7 0.2 - - - -
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.9 28.7 - - + -
16B ALA* 4.4 3.6 - - + -
17B THR* 4.4 10.5 - - + -
29B ILE* 3.9 31.2 - - + +
32B ILE* 3.9 36.8 - - + -
50B ILE* 3.8 26.0 - - + -
64B GLN 3.2 14.1 + - - +
65B ALA 3.5 8.5 - - - +
67B THR* 1.4 74.3 - - - +
69B LEU* 1.3 63.6 + - - +
71B ALA* 3.2 5.5 + - - +
72B CYS* 3.0 32.7 + - - -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.7 28.9 - - + -
50B ILE* 3.9 16.1 - - + +
51B MET* 4.0 18.2 - - - -
54B VAL* 4.9 0.4 - - + -
65B ALA 2.9 16.8 + - - +
66B LEU* 3.5 28.7 - - + +
68B LEU* 1.3 76.4 - - - +
70B GLY* 1.3 61.9 + - - +
72B CYS* 3.3 3.5 + - - +
73B VAL* 3.1 26.4 + - + +
80B PHE* 4.2 12.8 - - + -
84B VAL* 4.5 2.7 - - + -
89B PHE* 4.2 8.1 - - + -
108B LEU* 4.5 4.3 - - + -
111B LEU* 4.4 2.7 - - + -
115B TRP* 3.7 28.0 - - + -
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Residues in contact with GLY 70 (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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66B LEU 2.9 15.6 + - - -
67B THR* 3.9 2.5 - - - -
69B LEU* 1.3 74.7 - - - +
71B ALA* 1.3 56.0 + - - +
73B VAL* 3.3 4.0 + - - +
74B SER* 2.9 33.0 + - - -
107B LYS* 5.9 0.2 - - - -
111B LEU* 3.8 23.3 - - - +
115B TRP* 4.5 6.9 + - - -
47E GLY* 5.6 1.6 - - - -
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Residues in contact with ALA 71 (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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26B TRP* 4.4 5.4 - - + -
29B ILE* 3.5 30.3 - - + -
33B CYS* 4.0 2.7 - - - -
67B THR 3.0 18.8 + - - +
68B LEU 3.2 3.1 + - - +
70B GLY* 1.3 75.0 - - - +
72B CYS* 1.3 52.7 + - - +
74B SER* 3.3 2.0 + - - -
75B ASN* 2.8 44.2 + - - +
47E GLY* 3.9 22.8 - - - +
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Residues in contact with CYS 72 (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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32B ILE* 4.4 3.1 - - - -
33B CYS* 4.1 14.1 - - - -
36B VAL* 4.8 0.7 - - - -
46B CYS* 4.1 14.4 - - - -
50B ILE* 3.7 20.6 - - - -
68B LEU* 3.0 23.6 + - - +
69B LEU* 3.5 9.6 - - - +
71B ALA* 1.3 71.6 - - - +
73B VAL* 1.3 59.9 + - - +
76B CYS* 2.8 47.7 + - - +
80B PHE* 3.6 28.4 - - + +
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Residues in contact with VAL 73 (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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69B LEU* 3.1 14.2 + - + +
70B GLY 3.7 7.0 - - - +
72B CYS* 1.3 74.4 - - - +
74B SER* 1.3 61.9 + - - +
76B CYS 4.3 1.2 + - - -
77B GLY 4.6 0.3 + - - -
80B PHE* 3.9 20.9 - - + -
81B HIS* 2.9 44.8 - - + +
84B VAL* 4.3 9.0 - - + -
115B TRP* 3.4 55.4 - - + +
118B GLU* 4.0 11.6 - - - +
119B PHE* 4.1 5.6 - - + -
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLY 2.9 18.2 + - - -
71B ALA* 3.5 8.1 - - - -
72B CYS 3.3 0.2 - - - -
73B VAL* 1.3 78.0 - - - +
75B ASN* 1.3 57.3 + - - +
77B GLY 5.3 0.9 + - - -
118B GLU* 5.2 5.7 + - - -
46E ALA 4.1 11.4 + - - -
48E LYS* 3.1 57.6 + - - +
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Residues in contact with ASN 75 (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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30B LEU* 4.0 10.1 - - - +
33B CYS* 3.9 23.1 - - + +
71B ALA* 2.8 23.1 + - - +
74B SER* 1.3 73.3 - - - +
76B CYS* 1.3 60.8 + - - +
77B GLY 3.5 3.2 + - - -
47E GLY 2.8 24.6 + - - -
48E LYS* 3.2 18.6 + - - +
49E GLN* 2.8 34.5 + - + +
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Residues in contact with CYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B CYS* 3.7 38.6 - - - +
36B VAL* 3.9 21.3 - - + -
72B CYS* 2.8 44.1 + - - +
75B ASN* 1.3 72.3 - - - +
77B GLY* 1.3 65.8 + - - +
79B ILE* 3.3 19.9 - - - +
80B PHE* 3.6 15.0 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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