Contacts of the helix formed by residues 60 - 79 (chain B) in PDB entry 4L2A
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 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B SER* 1.3 76.5 - - - +
61B GLY* 1.3 75.3 + - - +
62B GLY 3.4 0.9 + - - -
63B VAL* 3.5 6.8 + - - +
64B PHE* 3.2 18.0 + - - -
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASP* 1.3 84.1 + - - +
62B GLY* 1.3 58.4 + - - -
64B PHE* 3.4 1.5 - - - +
65B ASN* 3.0 36.6 + - - +
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Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.7 12.3 - - - -
60B ASP 3.4 0.4 + - - -
61B GLY* 1.3 69.4 - - - -
63B VAL* 1.3 65.1 + - - +
65B ASN* 3.9 7.7 - - - +
66B ASN* 2.9 32.0 + - - +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.7 15.1 - - + +
41B LEU* 3.7 34.3 - - + +
42B ILE* 4.5 2.2 - - + -
45B THR* 5.9 2.9 - - + +
47B PHE* 4.1 24.5 - - + -
55B ILE* 3.5 28.0 - - + -
59B SER* 3.9 10.3 - - - -
60B ASP 3.5 6.4 + - - +
61B GLY 3.4 0.6 - - - -
62B GLY* 1.3 75.6 - - - +
64B PHE* 1.3 59.3 + - - +
67B ALA* 2.9 28.8 + - - +
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 3.3 31.2 - - + -
59B SER* 3.4 20.7 + - - +
60B ASP* 3.2 24.5 + - - -
61B GLY 3.4 8.1 - - - +
63B VAL* 1.3 77.4 - - - +
65B ASN* 1.3 80.4 + - - +
66B ASN 3.1 0.2 + - - -
67B ALA* 4.8 1.8 - - - -
68B ALA* 2.8 54.0 + - + +
141B ALA* 3.7 20.4 - - + -
142B ALA* 4.0 13.5 - - + -
143B THR* 4.2 7.9 - - + -
146B THR* 4.0 15.0 - - + -
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Residues in contact with ASN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 3.4 53.8 - - + +
61B GLY* 3.0 24.0 + - - +
62B GLY* 3.4 7.8 + - - +
64B PHE* 1.3 89.6 - - - +
66B ASN* 1.3 58.9 + - - +
69B GLN* 3.1 32.6 + - - +
140B ASN* 5.6 0.3 - - - +
141B ALA* 3.6 9.6 + - - +
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Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 5.7 1.6 - - - -
34B TYR* 3.3 42.3 - - - +
37B LYS* 3.3 42.8 - - - +
38B LEU* 4.1 13.0 - - + +
41B LEU* 4.0 7.3 - - + +
62B GLY* 2.9 25.5 + - - +
63B VAL 4.1 1.1 - - - +
65B ASN* 1.3 76.3 - - - +
67B ALA* 1.3 66.3 + - - +
69B GLN 3.3 0.9 + - - -
70B ILE* 3.0 28.0 + - - +
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Residues in contact with ALA 67 (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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38B LEU* 4.0 13.9 - - + +
52B LEU* 3.4 26.0 - - + +
55B ILE* 3.7 21.1 - - + -
56B VAL* 3.4 21.8 - - + +
63B VAL 2.9 21.4 + - - +
64B PHE 4.1 0.9 - - - +
66B ASN* 1.3 72.6 - - - +
68B ALA* 1.3 62.3 + - - +
70B ILE* 3.2 2.0 + - - +
71B TRP 3.1 17.3 + - - -
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Residues in contact with ALA 68 (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* 3.5 10.2 - - + +
64B PHE* 2.8 45.6 + - + +
67B ALA* 1.3 70.3 - - - +
69B GLN* 1.3 59.9 + - - +
71B TRP* 3.1 3.6 + - - +
72B ASN* 2.8 36.6 + - - +
141B ALA* 3.3 25.4 - - + +
143B THR* 4.3 7.0 - - + -
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 3.9 4.3 - - + -
34B TYR* 3.2 53.4 + - + -
65B ASN 3.1 21.4 + - - +
66B ASN 3.8 0.2 - - - +
68B ALA* 1.3 76.4 - - - +
70B ILE* 1.3 63.9 + - - +
72B ASN* 3.0 28.3 + - - +
73B HIS* 2.8 48.8 + - - -
122B TRP* 3.2 12.2 + - - -
140B ASN 3.5 9.2 - - - +
141B ALA* 3.5 8.0 - - + -
159B TRP* 3.3 25.5 - - - +
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Residues in contact with ILE 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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2B PHE* 5.0 8.5 - - + -
3B GLU 5.3 2.2 - - - +
5B PRO* 5.3 5.2 - - + -
31B HIS* 3.2 18.8 + - - +
34B TYR* 3.7 28.9 - - + +
35B VAL* 3.8 22.0 - - + +
38B LEU* 3.6 31.6 - - + -
52B LEU* 3.8 18.4 - - + -
66B ASN 3.0 19.9 + - - +
67B ALA* 3.5 5.6 - - - +
68B ALA 3.1 0.2 - - - -
69B GLN* 1.3 75.9 - - - +
71B TRP* 1.3 64.7 + - - +
74B THR* 2.9 31.6 + - - +
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Residues in contact with TRP 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.0 18.8 - - + +
53B GLU* 3.2 38.1 + - + -
56B VAL* 4.4 7.6 - - + -
67B ALA 3.1 9.9 + - - +
68B ALA* 3.6 7.6 - - - +
70B ILE* 1.3 80.0 - - - +
72B ASN* 1.3 73.8 + - - +
74B THR* 3.1 8.7 + - - -
75B PHE* 2.9 60.3 + + - +
124B TRP* 3.8 18.6 - + - -
143B THR* 3.6 19.7 - - + -
145B LEU* 3.7 26.7 - - + -
152B PRO* 3.8 25.4 - - + -
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA 2.8 25.7 + - - +
69B GLN* 3.0 21.7 + - - +
71B TRP* 1.3 80.3 - - - +
73B HIS* 1.4 57.1 + - - +
75B PHE* 3.4 3.6 + - - +
76B TYR* 2.9 27.5 + - - +
122B TRP* 3.4 34.0 - - + +
124B TRP* 3.3 19.0 - - + -
141B ALA 3.1 22.8 + - - -
142B ALA 4.0 2.4 + - - -
143B THR* 3.2 23.2 + - - -
155B THR* 4.0 1.7 - - - +
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Residues in contact with HIS 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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26B HIS* 3.1 25.1 + + - -
30B HIS* 5.1 0.2 - - - +
31B HIS* 3.5 28.7 - + + +
34B TYR* 3.5 18.5 - + - -
69B GLN* 2.8 55.8 + - - +
72B ASN* 1.4 74.5 - - - +
74B THR* 1.3 66.6 + - - +
76B TYR* 3.2 6.5 + + - +
77B TRP* 3.0 34.9 + + - +
122B TRP* 3.6 9.8 - + - -
157B ASP* 3.3 4.4 + - - -
161B HIS* 3.7 1.8 + - - -
5001B FE 2.0 33.0 - - - -
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Residues in contact with THR 74 (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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5B PRO* 3.6 26.7 - - + +
31B HIS* 3.2 18.2 + - - -
52B LEU* 5.7 0.7 - - - +
70B ILE* 2.9 17.9 + - - +
71B TRP* 3.1 12.6 + - - -
73B HIS* 1.3 79.0 - - - +
75B PHE* 1.3 61.5 + - - +
77B TRP* 3.5 7.4 + - + +
78B ASN* 3.2 36.9 + - - +
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Residues in contact with PHE 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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71B TRP* 2.9 48.1 + + + +
72B ASN* 3.5 5.4 - - - +
74B THR* 1.3 79.8 - - - +
76B TYR* 1.3 59.5 + - - +
78B ASN* 3.4 7.4 + - - +
79B SER* 2.9 27.0 + - - -
124B TRP* 3.7 16.4 - + - -
152B PRO* 3.4 38.8 - - + -
153B ILE 3.6 2.5 - - - -
154B LEU* 3.6 26.2 - - - -
155B THR* 4.0 7.4 - - + -
186B PHE* 3.5 24.0 - + - -
190B ASN* 3.4 17.3 - - - -
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Residues in contact with TYR 76 (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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18B ILE* 3.9 15.8 - - - +
26B HIS* 3.7 16.3 + + - -
72B ASN 2.9 17.7 + - - +
73B HIS* 3.4 6.7 - + - +
75B PHE* 1.3 74.7 - - - +
77B TRP* 1.3 97.1 + + - +
79B SER* 2.8 23.6 + - - -
80B LEU* 3.5 28.3 - - + +
122B TRP* 3.8 5.8 - + + -
155B THR* 3.5 23.3 - - + +
156B VAL* 4.1 5.4 - - + -
157B ASP* 3.4 37.5 - - + -
162B ALA* 4.2 7.3 + - - +
174B TYR* 2.8 25.5 + - - -
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Residues in contact with TRP 77 (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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5B PRO* 5.9 2.0 - - + -
6B SER 5.7 1.8 - - - -
7B LEU* 3.6 21.3 - - + -
8B PRO* 3.9 17.0 - - + -
9B TYR* 2.7 40.3 + - - +
18B ILE* 6.1 0.4 - - + -
23B LEU* 3.5 26.2 - - + -
26B HIS* 3.4 43.5 - + + -
27B HIS* 3.5 30.1 + + + -
31B HIS* 2.8 33.6 + + - -
73B HIS* 3.0 29.9 + + + +
74B THR* 3.9 7.0 - - + +
76B TYR* 1.3 100.2 - + - +
78B ASN* 1.3 58.8 + - - +
79B SER 3.4 0.2 + - - -
80B LEU* 3.1 18.6 + - + +
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Residues in contact with ASN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 3.5 25.2 - - - +
74B THR* 3.2 24.3 + - - +
75B PHE* 3.6 4.1 - - - +
76B TYR 3.1 0.6 - - - -
77B TRP* 1.3 76.7 - - - +
79B SER* 1.3 55.5 + - - +
80B LEU 3.1 6.9 + - - -
183B ASN* 2.9 28.7 + - - +
186B PHE* 3.3 43.4 - - + +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 2.9 16.5 + - - -
76B TYR 2.8 12.7 + - - -
78B ASN* 1.3 75.1 - - - +
80B LEU* 1.3 59.1 + - - +
154B LEU* 3.6 27.3 - - - +
155B THR 3.1 37.8 + - - -
178B PHE* 4.2 3.0 - - - -
182B VAL* 3.5 8.5 - - - +
183B ASN* 2.8 24.7 + - - -
186B PHE* 3.9 4.1 - - - -
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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