Contacts of the helix formed by residues 74 - 90 (chain D) in PDB entry 1LBH
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 HIS 74 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C HIS* 3.5 39.3 + + + -
277C GLU* 6.0 2.9 - - + -
278C ASP* 3.1 26.0 + - - -
72D ALA 3.9 8.8 + - - -
73D LEU* 1.3 74.3 - - - +
75D ALA* 1.3 66.5 + - - +
77D SER* 3.4 5.7 + - - -
78D GLN* 3.0 32.6 + - + +
248D GLN* 3.3 40.8 + - + +
276D THR* 4.1 26.7 - - + +
278D ASP* 3.9 10.0 + - - -
282D TYR* 4.7 4.7 - - - -
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU* 4.7 0.2 - - - +
74D HIS* 1.3 76.6 - - - +
76D PRO* 1.4 71.3 - - + +
78D GLN* 2.8 18.6 + - - +
79D ILE* 3.0 17.8 + - + +
248D GLN* 5.2 0.4 + - - -
274D ASP* 4.0 16.4 - - - +
276D THR* 4.3 5.7 - - + +
293D PHE* 4.0 21.5 - - + -
400D IPT 4.0 25.1 - - - +
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Residues in contact with PRO 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D THR* 3.9 9.9 + - - +
69D SER* 4.3 10.1 - - - -
70D SER 2.9 29.4 - - - +
71D LEU* 3.8 4.5 - - + -
73D LEU* 3.2 26.9 - - + +
75D ALA* 1.4 91.8 - - + +
77D SER* 1.3 53.8 + - - +
79D ILE* 3.7 4.8 + - + +
80D VAL* 3.1 32.1 + - - +
125D ASN* 3.7 25.1 + - - +
400D IPT 4.4 13.6 - - + +
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Residues in contact with SER 77 (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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71C LEU* 3.4 32.3 + - - +
72C ALA* 4.3 3.0 + - - -
77C SER* 4.2 1.7 + - - -
71D LEU* 2.7 43.6 + - - +
73D LEU 3.1 7.4 + - - -
74D HIS* 3.4 10.0 + - - -
75D ALA 3.0 0.6 - - - -
76D PRO* 1.3 74.4 - - - +
78D GLN* 1.3 60.7 + - - +
79D ILE 3.2 1.6 - - - -
80D VAL* 3.6 4.4 + - - +
81D ALA* 3.2 25.5 + - - +
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Residues in contact with GLN 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ALA* 4.8 15.5 - - + +
74D HIS* 3.0 22.9 + - + +
75D ALA* 2.8 7.4 + - - +
77D SER* 1.3 75.8 - - - +
79D ILE* 1.3 60.7 + - - +
81D ALA* 3.6 7.0 - - - +
82D ALA* 3.1 25.1 + - - +
275D ASP 4.9 0.4 + - - -
276D THR* 3.1 19.4 - - - +
277D GLU* 3.0 47.7 + - + +
293D PHE* 3.7 31.9 - - + +
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Residues in contact with ILE 79 (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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75D ALA 3.0 18.9 + - - +
76D PRO* 3.9 5.2 - - + +
78D GLN* 1.3 77.0 - - - +
80D VAL* 1.3 56.8 + - + +
81D ALA 3.2 0.2 - - - -
82D ALA* 3.2 5.6 + - - +
83D ILE* 2.7 53.3 + - + +
125D ASN* 4.4 25.1 - - + +
148D LEU* 3.9 20.9 - - + -
293D PHE* 3.5 38.1 - - + +
296D LEU* 4.1 20.4 - - + -
297D GLY* 5.2 1.8 - - - -
400D IPT 4.6 13.2 - - - +
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 4.8 5.8 - - + -
98C MET* 3.9 22.2 - - + -
66D VAL* 4.8 7.2 - - + -
68D THR* 4.0 23.3 - - + +
71D LEU* 4.1 11.9 - - + -
76D PRO 3.1 19.6 + - - +
77D SER* 3.6 6.0 + - - +
78D GLN 3.5 0.2 - - - -
79D ILE* 1.3 76.0 - - + +
81D ALA* 1.3 56.4 + - - +
83D ILE* 2.9 10.5 + - + +
84D LYS* 2.7 32.9 + - - +
94D VAL* 5.2 2.7 - - + -
96D VAL* 3.5 30.5 - - + -
125D ASN* 5.6 0.4 - - - +
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Residues in contact with ALA 81 (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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70C SER* 4.8 7.4 - - - +
71C LEU* 5.1 0.8 - - + +
72C ALA* 4.3 20.0 - - + +
98C MET* 4.6 15.0 - - + +
77D SER 3.2 16.0 + - - +
78D GLN* 3.6 7.2 - - - +
79D ILE 3.2 0.2 - - - -
80D VAL* 1.3 80.9 - - - +
82D ALA* 1.3 56.7 + - - +
84D LYS* 3.5 2.2 + - - +
85D SER* 2.8 30.3 + - - -
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Residues in contact with ALA 82 (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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78D GLN 3.1 10.4 + - - +
79D ILE 3.6 5.6 - - - +
80D VAL 3.2 0.2 - - - -
81D ALA* 1.3 75.7 - - - +
83D ILE* 1.3 58.8 + - - +
85D SER* 2.9 8.7 + - - -
86D ARG* 2.7 35.7 + - - +
293D PHE 3.2 27.4 - - - +
294D ARG* 3.9 17.0 - - + +
297D GLY* 3.8 10.1 - - - -
298D GLN 5.1 0.2 - - - +
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Residues in contact with ILE 83 (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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64D ILE* 5.1 1.3 - - + -
66D VAL* 3.7 33.2 - - + -
79D ILE* 2.7 42.4 + - + +
80D VAL* 2.9 12.3 + - - +
82D ALA* 1.3 70.8 - - - +
84D LYS* 1.3 62.1 + - - +
87D ALA* 3.1 22.0 + - - +
94D VAL* 3.9 10.8 - - + -
123D ILE* 3.6 34.5 - - + -
148D LEU* 4.7 0.7 - - + -
297D GLY* 4.0 22.9 - - - +
300D SER* 4.0 6.7 - - - +
301D VAL* 3.5 13.3 - - + +
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Residues in contact with LYS 84 (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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97C SER* 6.2 0.4 - - - -
98C MET* 3.7 40.2 - - + +
100C GLU* 3.6 13.5 - - + +
80D VAL 2.7 17.3 + - - +
81D ALA* 3.8 4.7 - - - +
83D ILE* 1.3 70.0 - - - +
85D SER* 1.3 57.7 + - - +
86D ARG 2.7 2.8 + - - -
87D ALA 2.8 2.4 + - - -
88D ASP* 2.6 58.0 + - - +
92D ALA 3.1 24.9 + - - -
93D SER* 3.6 5.9 + - - +
94D VAL* 3.4 40.2 + - + +
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ALA 2.8 22.5 + - - -
82D ALA* 3.4 9.6 - - - -
84D LYS* 1.3 73.7 - - - +
86D ARG* 1.3 60.8 + - - +
88D ASP* 3.2 19.1 - - - +
89D GLN* 3.3 20.8 + - - +
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Residues in contact with ARG 86 (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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82D ALA 2.7 17.4 + - - +
83D ILE 3.8 4.5 - - - +
84D LYS 2.7 3.8 + - - -
85D SER* 1.3 67.7 - - - +
87D ALA* 1.3 57.5 + - - +
88D ASP 2.9 4.0 - - - -
89D GLN* 2.8 56.0 + - - +
90D LEU* 3.4 27.7 - - - +
298D GLN* 3.1 49.5 + - + +
301D VAL* 3.9 11.0 - - + -
302D ASP* 2.5 46.6 + - - -
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Residues in contact with ALA 87 (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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64D ILE* 4.0 10.5 - - + -
83D ILE 3.1 7.2 + - - +
84D LYS* 2.8 4.9 + - + +
86D ARG* 1.3 75.9 - - - +
88D ASP* 1.3 58.3 + - - +
90D LEU* 3.5 9.2 + - - -
91D GLY 3.4 3.1 + - - -
92D ALA* 2.8 52.2 + - + +
94D VAL* 3.2 35.9 - - + -
301D VAL* 4.2 2.0 - - + +
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Residues in contact with ASP 88 (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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100C GLU* 2.9 46.0 - - - +
84D LYS* 2.6 36.9 + - - +
85D SER* 3.2 14.9 - - - +
87D ALA* 1.3 74.7 - - - +
89D GLN* 1.3 59.5 + - + +
91D GLY* 3.7 8.5 + - - -
92D ALA 4.6 3.1 - - - +
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Residues in contact with GLN 89 (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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85D SER* 3.3 24.9 + - - +
86D ARG* 2.8 39.6 + - - +
88D ASP* 1.3 78.4 - - + +
90D LEU* 1.3 69.3 + - + +
91D GLY 3.2 5.6 + - - -
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Residues in contact with LEU 90 (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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62D LEU* 5.4 6.6 - - + +
86D ARG* 3.4 51.5 + - - +
87D ALA* 3.5 5.9 + - - +
88D ASP 3.5 0.4 - - - -
89D GLN* 1.3 86.9 - - + +
91D GLY* 1.3 63.4 + - - +
92D ALA* 4.6 6.9 - - + +
301D VAL* 4.0 19.5 - - + -
302D ASP* 4.1 9.6 - - - +
305D LEU* 4.3 17.9 - - + -
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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