Contacts of the helix formed by residues 87 - 99 (chain N) in PDB entry 3LEL
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 87 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44M GLY* 4.9 4.5 - - - -
46M GLY* 5.6 0.2 - - - -
47M ALA* 3.8 8.3 - - - +
85N THR* 3.9 17.9 - - + +
86N ILE* 1.3 77.3 - - - +
88N SER* 1.3 66.4 + - - +
89N ARG* 3.0 26.6 + - - +
90N GLU* 2.7 27.8 + - - +
91N ILE* 3.3 21.0 + - - +
-34S G 5.9 1.6 - - - +
-33S A 6.0 1.3 - - - +
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Residues in contact with SER 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M GLY* 3.7 24.8 - - - -
47M ALA* 3.4 14.3 - - - +
50M TYR* 3.4 27.9 - - - -
87N THR* 1.3 74.0 - - - +
89N ARG* 1.3 54.8 + - - +
91N ILE* 3.1 5.7 + - - +
92N GLN* 2.8 31.2 + - - +
115N VAL* 4.4 12.2 - - - +
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Residues in contact with ARG 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L GLU 3.5 15.6 + - - -
75L HIS* 2.7 61.3 + - + +
77L LYS* 3.6 35.0 - - - +
87N THR* 3.0 13.4 + - - +
88N SER* 1.3 81.5 + - - +
90N GLU* 1.3 66.5 + - - +
92N GLN* 3.1 22.8 + - + +
93N THR* 3.1 17.8 + - - +
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Residues in contact with GLU 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L HIS* 3.0 36.4 + - + +
74N ALA* 4.1 30.3 - - + +
77N LEU* 3.7 8.0 - - + +
78N ALA* 4.6 8.3 - - - +
83N ARG* 5.0 9.1 - - - +
85N THR 2.9 15.7 - - - +
86N ILE* 4.2 8.7 - - + -
87N THR* 2.7 45.2 + - - +
89N ARG* 1.3 81.0 - - - +
91N ILE* 1.3 63.7 + - - +
92N GLN 3.2 0.3 + - - -
93N THR* 3.2 3.6 + - - -
94N ALA* 2.9 23.9 + - - +
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Residues in contact with ILE 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M LEU* 5.1 5.4 - - + -
47M ALA* 3.8 27.6 - - + +
50M TYR* 3.7 24.9 - - + -
51M LEU* 4.0 39.5 - - + +
54M VAL* 4.7 0.4 - - + -
70N ILE* 4.4 13.2 - - + -
71N ALA* 5.6 1.6 - - - -
74N ALA* 4.6 7.2 - - + -
86N ILE* 4.3 10.3 - - + -
87N THR 3.3 13.2 + - - +
88N SER 3.1 8.0 + - - +
90N GLU* 1.3 74.9 - - - +
92N GLN* 1.3 57.5 + - - +
94N ALA* 3.4 6.8 + - - +
95N VAL* 2.8 41.6 + - + +
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Residues in contact with GLN 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M TYR* 3.1 42.8 + - + +
88N SER 2.8 11.3 + - - +
89N ARG* 3.1 16.7 + - + +
91N ILE* 1.3 73.2 - - - +
93N THR* 1.3 57.6 + - - +
95N VAL* 3.1 7.6 + - - +
96N ARG* 2.9 66.0 + - - +
108N VAL* 3.7 7.7 - - + +
112N THR* 3.6 17.2 + - - +
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Residues in contact with THR 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L THR* 3.7 26.0 - - + +
75L HIS* 2.5 41.5 + - + +
77N LEU* 3.7 19.1 - - + -
89N ARG* 3.1 10.5 + - - +
90N GLU 3.7 4.5 - - - -
92N GLN* 1.3 75.3 - - - +
94N ALA* 1.3 53.3 + - - +
96N ARG* 2.8 14.9 + - - +
97N LEU* 2.6 41.3 + - + +
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Residues in contact with ALA 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N ILE* 3.6 31.1 - - + +
73N GLU* 3.8 10.1 - - + +
74N ALA* 3.8 17.3 - - + +
77N LEU* 3.6 7.3 - - + +
90N GLU 2.9 16.5 + - - +
91N ILE* 3.4 7.2 - - - +
93N THR* 1.3 76.3 - - - +
95N VAL* 1.3 55.8 + - - +
97N LEU* 3.8 4.8 - - - +
98N LEU* 3.0 30.3 + - - +
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Residues in contact with VAL 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M TYR* 4.5 2.0 - - + -
54M VAL* 4.1 20.9 - - + -
70N ILE* 4.3 11.4 - - + -
91N ILE* 2.8 41.0 + - + +
92N GLN* 3.3 9.2 - - - +
93N THR 3.0 0.2 - - - -
94N ALA* 1.3 74.3 - - - +
96N ARG* 1.3 63.2 + - - +
97N LEU 3.2 0.2 - - - -
98N LEU* 4.8 1.1 - - - -
99N LEU* 2.9 51.8 + - + +
104N ALA* 4.3 2.5 - - - +
107N ALA* 3.8 22.9 - - + -
108N VAL* 4.3 13.2 - - + +
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Residues in contact with ARG 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L ARG* 6.0 2.1 - - - -
68L ASP* 5.5 1.2 - - - +
71L THR* 4.5 17.3 - - + +
92N GLN* 2.9 51.3 + - - +
93N THR* 2.8 14.4 + - - +
95N VAL* 1.3 77.9 - - - +
97N LEU* 1.3 61.9 + - - +
99N LEU 3.5 11.8 - - - +
104N ALA* 4.5 13.6 - - + +
108N VAL* 3.5 28.4 - - + +
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Residues in contact with LEU 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L ASP* 3.9 35.3 - - + +
71L THR* 3.7 31.0 - - + -
72L TYR* 3.8 34.3 - - + +
92L ARG* 3.1 33.3 + - - +
73N GLU* 3.8 13.7 - - - +
77N LEU* 4.2 16.6 - - + -
93N THR* 2.6 25.7 + - + +
94N ALA* 3.8 6.1 - - - +
96N ARG* 1.3 75.8 - - - +
98N LEU* 1.3 59.6 + - - +
99N LEU 4.8 0.3 - - - +
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Residues in contact with LEU 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L ARG* 3.9 14.8 + - - +
96M LEU* 4.2 14.4 - - + +
66N VAL* 4.7 4.9 - - + +
69N ARG* 3.6 55.6 - - + +
70N ILE* 3.9 17.7 - - + -
73N GLU* 4.7 7.4 - - + +
94N ALA 3.0 17.9 + - - +
95N VAL* 4.3 1.1 - - - +
97N LEU* 1.3 80.4 - - - +
99N LEU* 1.3 83.9 + - + +
100N PRO* 3.9 2.1 - - - +
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Residues in contact with LEU 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M LEU* 3.8 37.9 - - + -
96M LEU* 3.8 15.7 - - + -
66N VAL* 5.4 0.4 - - + -
70N ILE* 5.1 4.3 - - + -
95N VAL* 2.9 25.4 + - + +
96N ARG 3.5 10.4 - - - +
97N LEU 4.8 0.3 - - - +
98N LEU* 1.3 101.1 - - + +
100N PRO* 1.3 71.1 - - + +
101N GLY 3.8 0.7 + - - -
103N LEU* 3.9 11.4 - - + +
104N ALA* 3.5 19.5 - - - +
107N ALA* 3.6 31.0 - - + -
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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
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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