Contacts of the helix formed by residues 62 - 82 (chain B) in PDB entry 4L1O
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 GLU 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.7 22.5 - - - +
51B LEU* 5.7 0.2 - - - +
53B LYS* 4.2 8.1 + - - +
57B ASN 4.5 1.3 - - - +
58B ALA* 3.5 12.5 + - - +
59B TYR 3.3 2.0 + - - -
60B TYR 3.6 0.6 - - - -
61B GLU* 1.3 82.1 - - - +
63B VAL* 1.3 69.4 + - + +
64B VAL 3.3 1.6 - - - -
65B TYR* 3.3 23.3 + - - +
66B VAL* 3.7 5.7 + - - +
114B ASN 4.7 0.7 - - - +
115B TYR* 3.0 35.8 - - + -
116B PRO* 3.2 2.2 - - - +
117B PHE* 2.8 38.6 + - + +
118B ASN* 3.1 24.5 + - + +
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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
----------------------------------------------------------
36B ILE* 3.5 31.6 - - + +
43B LEU* 4.7 16.8 - - + -
47B LEU* 4.8 10.1 - - + -
58B ALA* 3.0 23.1 + - + +
59B TYR* 3.1 21.3 + - + -
62B GLU* 1.3 78.1 - - + +
64B VAL* 1.3 62.6 + - - +
66B VAL* 3.1 13.9 + - - +
67B LEU* 3.2 10.0 + - - +
117B PHE* 3.9 30.7 - - + -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 2.8 58.1 + - + +
60B TYR* 4.0 24.0 - - + +
63B VAL* 1.3 73.9 - - - +
65B TYR* 1.3 80.8 + - + +
67B LEU* 3.2 6.8 + - + +
68B GLU* 2.8 49.5 + - + +
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Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR 3.7 25.0 + - - -
61B GLU* 4.0 6.2 - - - -
62B GLU* 3.3 19.0 + - - +
63B VAL 3.2 0.6 - - - -
64B VAL* 1.3 82.0 - - + +
66B VAL* 1.3 64.6 + - - +
68B GLU* 4.0 19.9 - - - +
69B GLU* 3.1 23.6 + - - +
118B ASN* 3.9 12.8 - - - +
122B GLN* 3.9 11.6 + - - +
395B THR* 3.7 44.3 + - + +
397B HIS* 5.5 0.7 - - - -
601B 1VL 3.8 27.1 + - - -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 3.8 10.3 - - + -
62B GLU 4.0 7.0 - - - +
63B VAL 3.1 6.9 + - - +
65B TYR* 1.3 77.6 - - - +
67B LEU* 1.3 57.3 + - - +
69B GLU* 3.3 6.0 + - - +
70B ILE* 3.0 32.6 + - + +
117B PHE* 3.6 35.4 - - + +
118B ASN* 3.8 25.1 - - - +
121B ILE* 3.7 27.4 - - + -
122B GLN* 4.3 12.3 - - + +
125B VAL* 4.5 5.3 - - + +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 3.7 38.4 - - + +
36B ILE* 4.2 23.3 - - + +
59B TYR* 3.5 26.9 - - + +
63B VAL* 3.2 11.5 + - + +
64B VAL* 3.2 10.3 + - + +
66B VAL* 1.3 78.0 - - - +
68B GLU* 1.3 57.6 + - + +
70B ILE* 3.2 6.2 + - + +
71B GLU* 3.0 30.3 + - + +
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 2.8 35.9 + - + +
65B TYR* 4.0 25.8 - - - +
67B LEU* 1.3 77.4 - - + +
69B GLU* 1.3 57.5 + - - +
71B GLU* 4.0 16.0 - - - +
72B TYR* 3.1 29.5 + - - +
395B THR 5.7 0.5 - - - +
397B HIS* 3.5 21.1 + - + +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TYR 3.1 19.9 + - - +
66B VAL* 3.6 5.2 - - - +
68B GLU* 1.3 76.0 - - - +
70B ILE* 1.3 61.0 + - - +
72B TYR* 3.4 4.3 + - - +
73B MET* 2.9 64.0 + - + +
122B GLN* 3.6 31.0 - - + +
125B VAL* 4.1 9.9 - - + -
397B HIS* 3.8 17.2 + - + -
413B HIS* 3.4 11.0 - - - +
414B GLY* 3.0 32.1 + - - -
417B SER* 4.2 1.2 + - - -
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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
----------------------------------------------------------
29B LEU* 3.5 24.0 - - + +
32B LEU* 3.6 31.0 - - + -
33B GLN* 3.5 28.9 - - + +
36B ILE* 4.2 15.5 - - + -
66B VAL* 3.0 21.6 + - + +
67B LEU* 3.2 7.8 + - - +
69B GLU* 1.3 76.4 - - - +
71B GLU* 1.3 57.9 + - - +
73B MET* 3.8 1.3 - - - +
74B ILE* 2.9 44.3 + - + +
125B VAL* 3.6 30.7 - - + -
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 4.6 9.9 - - - +
67B LEU* 3.0 18.8 + - + +
68B GLU* 4.0 16.0 - - - +
70B ILE* 1.3 77.8 - - - +
72B TYR* 1.3 62.6 + - - +
74B ILE* 3.6 6.2 + - - +
75B GLN* 3.2 34.9 + - - +
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Residues in contact with TYR 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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87A GLU* 5.3 6.9 + - - -
68B GLU 3.1 20.5 + - - +
69B GLU* 3.7 12.6 - - - +
71B GLU* 1.3 78.0 - - - +
73B MET* 1.3 63.0 + - - +
75B GLN* 3.0 35.1 - - - +
76B LYS* 3.1 37.7 + - + +
80B TRP* 3.7 32.2 - + - -
397B HIS* 3.7 53.7 + + + +
398B SER* 5.7 1.0 - - - -
414B GLY* 3.8 9.9 - - - -
415B LYS* 4.4 2.5 + - - +
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Residues in contact with MET 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.8 4.5 - - + -
69B GLU* 2.9 61.1 + - + +
70B ILE 3.9 2.5 - - - +
72B TYR* 1.3 69.8 - - + +
74B ILE* 1.3 60.8 + - - +
77B LEU* 2.8 34.8 + - - +
80B TRP* 3.9 24.9 - - + -
122B GLN 5.2 0.2 - - - +
125B VAL* 4.0 9.6 - - + -
126B GLY* 3.8 23.1 - - - +
129B ALA* 3.8 21.3 - - + -
414B GLY 3.5 8.1 - - - +
417B SER* 3.5 28.9 - - - +
418B PHE* 5.3 1.8 - - - -
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 4.4 29.1 - - + +
29B LEU* 3.9 24.7 - - + -
30B GLU* 3.9 30.1 - - + +
33B GLN* 4.0 9.4 - - - +
70B ILE* 2.9 39.8 + - + +
71B GLU* 3.8 6.7 - - - +
73B MET* 1.3 78.5 - - - +
75B GLN* 1.3 66.3 + - + +
77B LEU* 3.5 13.7 + - - +
78B PRO* 3.8 6.1 - - - +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLU* 3.2 25.8 + - - +
72B TYR* 3.0 40.4 - - - +
74B ILE* 1.3 82.5 - - + +
76B LYS* 1.3 72.3 + - + +
78B PRO* 3.8 9.2 - - - +
79B GLU* 4.5 6.8 - - - +
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Residues in contact with LYS 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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87A GLU* 5.1 12.7 + - - -
72B TYR* 3.1 45.4 + - + +
75B GLN* 1.3 86.0 - - + +
77B LEU* 1.3 65.9 + - - +
78B PRO* 3.3 4.3 - - - -
79B GLU* 3.0 43.7 + - - +
80B TRP* 3.0 51.0 + - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.1 22.0 - - + +
25B ARG* 4.0 24.0 - - + -
26B ILE* 4.1 20.2 - - + -
29B LEU* 4.7 8.5 - - + -
73B MET 2.8 18.0 + - - +
74B ILE 3.5 5.1 + - - +
76B LYS* 1.3 75.0 - - - +
78B PRO* 1.4 63.6 - - + +
80B TRP* 3.2 6.2 + - + +
81B ALA* 2.8 33.8 + - + +
129B ALA* 3.2 36.3 - - + +
418B PHE* 3.7 20.9 - - + -
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Residues in contact with PRO 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.9 22.5 - - + +
26B ILE* 5.4 7.6 - - + -
74B ILE 3.8 9.6 - - - +
75B GLN 3.8 8.5 - - - +
76B LYS 3.4 4.7 - - - -
77B LEU* 1.4 95.2 - - + +
79B GLU* 1.3 60.8 + - + +
81B ALA* 4.1 0.7 - - - +
82B ALA* 3.3 23.0 + - - +
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Residues in contact with GLU 79 (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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75B GLN 4.5 4.7 - - - +
76B LYS* 3.0 42.9 + - - +
78B PRO* 1.3 77.2 - - + +
80B TRP* 1.3 69.7 + - + +
82B ALA* 3.4 12.1 + - - +
602B K 2.8 19.2 - - - -
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Residues in contact with TRP 80 (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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72B TYR* 3.7 25.6 - + - -
73B MET* 3.9 27.4 - - + -
76B LYS* 3.0 48.9 + - + +
77B LEU* 3.9 9.2 - - + +
79B GLU* 1.3 81.8 + - + +
81B ALA* 1.3 60.7 + - - +
82B ALA 3.9 1.4 - - - +
101B SER* 4.0 6.1 + - - -
129B ALA* 5.8 0.7 - - + -
414B GLY* 3.6 15.7 - - - -
415B LYS* 3.5 65.6 + - + +
418B PHE* 3.3 50.7 - + + -
424B ARG* 5.9 0.3 + - - -
602B K 3.3 12.6 - - - -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.8 33.0 - - + -
25B ARG* 4.9 2.7 - - - +
77B LEU* 2.8 19.1 + - + +
78B PRO 4.2 0.9 - - - +
80B TRP* 1.3 76.2 - - - +
82B ALA* 1.3 65.0 + - - +
83B ASP* 3.6 3.1 + - - +
100B HIS* 5.9 0.5 + - - -
101B SER* 4.5 14.9 + - - +
418B PHE* 3.7 16.1 - - + -
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PRO 3.3 17.8 + - - +
79B GLU* 3.6 9.6 - - - +
80B TRP 3.3 2.8 - - - +
81B ALA* 1.3 80.2 - - - +
83B ASP* 1.3 72.5 + - - +
84B GLU* 3.4 0.9 + - - +
99B ILE 4.3 2.1 - - - +
101B SER* 5.1 4.1 + - - -
602B K 3.0 16.4 - - - -
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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