Contacts of the helix formed by residues 74 - 90 (chain A) in PDB entry 1LBI
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ALA 4.4 6.4 + - - -
73A LEU* 1.3 70.0 - - - +
75A ALA* 1.3 70.7 + - - +
77A SER* 3.1 15.2 + - - -
78A GLN* 3.2 15.4 + - - +
248A GLN* 2.8 40.8 + - + +
276A THR* 3.8 22.9 - - + -
278A ASP* 3.9 15.9 + - - -
282A TYR* 4.3 8.5 + - - -
72B ALA* 4.8 2.3 - - - +
74B HIS* 3.2 38.1 + + + -
277B GLU* 6.4 0.9 - - + -
278B ASP* 2.6 33.5 + - - -
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 4.7 0.2 - - - +
74A HIS* 1.3 76.6 - - - +
76A PRO* 1.4 64.0 - - + +
78A GLN* 3.1 8.9 + - - +
79A ILE* 3.1 32.5 + - + +
246A ASN* 6.0 1.6 - - - +
248A GLN* 4.5 1.4 + - - -
274A ASP* 3.6 25.6 - - - +
276A THR* 3.6 10.6 - - + +
293A PHE* 3.8 21.6 - - + -
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Residues in contact with PRO 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 4.5 6.1 - - - +
69A SER* 5.1 14.6 - - - +
73A LEU* 3.3 36.8 - - + +
75A ALA* 1.4 95.1 - - + +
77A SER* 1.3 55.9 + - - +
78A GLN 3.3 0.2 - - - -
79A ILE* 3.6 15.8 + - + +
80A VAL* 3.0 31.9 + - - +
125A ASN* 4.0 16.2 + - - +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ALA* 4.7 5.4 - - - -
73A LEU 3.2 13.4 + - - -
74A HIS* 3.1 11.2 + - - -
76A PRO* 1.3 75.0 - - - +
78A GLN* 1.3 59.4 + - - +
80A VAL* 3.5 9.5 + - - +
81A ALA* 3.0 21.8 + - - +
72B ALA* 3.4 22.9 - - - +
77B SER* 3.8 22.9 + - - -
98B MET* 5.1 2.1 - - - +
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A HIS* 3.2 11.0 + - - +
75A ALA 3.1 10.2 + - - +
77A SER* 1.3 74.3 - - - +
79A ILE* 1.3 60.7 + - - +
81A ALA* 3.3 6.7 + - + +
82A ALA* 3.0 26.5 + - - +
275A ASP 4.2 3.0 + - - -
276A THR* 3.6 12.8 - - - +
277A GLU* 3.1 63.4 + - - +
278A ASP* 5.5 0.7 - - - +
290A LYS* 5.9 0.8 - - - +
293A PHE* 3.0 42.0 - - + +
294A ARG* 4.7 2.3 + - - -
72B ALA* 3.6 13.2 - - + +
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ALA* 3.1 16.7 + - + +
76A PRO* 3.6 16.6 - - + +
77A SER 3.3 0.2 - - - -
78A GLN* 1.3 76.3 - - - +
80A VAL* 1.3 56.6 + - + +
82A ALA* 3.1 1.9 + - - +
83A ILE* 2.8 55.0 + - + +
125A ASN* 3.7 25.8 - - - +
148A LEU* 4.4 3.1 - - + -
293A PHE* 3.5 32.8 - - + -
296A LEU* 3.5 31.2 - - + -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.8 10.8 - - + -
68A THR* 3.4 29.8 - - + +
76A PRO 3.0 28.1 + - - +
77A SER* 3.7 8.5 - - - +
78A GLN 3.3 0.4 - - - -
79A ILE* 1.3 76.4 - - + +
81A ALA* 1.3 57.0 + - - +
83A ILE* 3.4 7.9 + - + +
84A LYS* 2.9 29.3 + - + +
94A VAL* 5.9 2.0 - - + +
96A VAL* 4.4 16.4 - - + -
125A ASN* 4.9 3.1 - - - +
98B MET* 3.6 27.6 - - + -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A SER 3.0 18.3 + - - +
78A GLN* 3.5 9.2 - - + +
79A ILE 3.2 0.4 - - - -
80A VAL* 1.3 75.6 - - - +
82A ALA* 1.3 56.6 + - - +
84A LYS* 3.8 1.9 - - - +
85A SER* 2.9 29.1 + - - -
294A ARG* 3.9 8.1 + - - +
70B SER* 3.2 31.8 + - - +
71B LEU* 4.4 1.1 - - - -
72B ALA* 4.1 11.9 - - + +
98B MET* 4.2 7.6 - - + +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLN 3.0 11.5 + - - +
79A ILE 3.5 5.8 - - - +
81A ALA* 1.3 76.7 - - - +
83A ILE* 1.3 64.2 + - - +
85A SER* 3.4 2.1 + - - -
86A ARG* 3.2 18.9 + - - +
293A PHE 2.7 35.0 - - - +
294A ARG* 3.4 27.9 + - - +
297A GLY* 3.3 14.5 - - - -
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 4.5 2.0 - - + -
66A VAL* 4.1 26.2 - - + -
79A ILE* 2.8 52.1 + - + +
80A VAL* 3.4 8.7 + - + +
82A ALA* 1.3 76.8 - - - +
84A LYS* 1.3 60.3 + - - +
87A ALA* 3.1 19.9 + - - +
94A VAL* 4.4 10.5 - - + -
123A ILE* 4.0 14.8 - - + -
148A LEU* 4.4 7.6 - - + -
296A LEU 3.8 3.6 - - - +
297A GLY* 3.6 19.7 - - - -
300A SER* 3.5 20.4 - - - +
301A VAL* 3.2 20.0 - - + +
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL 2.9 17.9 + - - +
81A ALA 4.1 2.2 - - - +
83A ILE* 1.3 76.1 - - - +
85A SER* 1.3 65.1 + - - +
86A ARG 3.2 0.2 - - - -
87A ALA* 3.8 11.7 - - + -
88A ASP* 3.0 48.9 + - - +
94A VAL* 4.2 20.4 - - + +
70B SER* 3.5 19.3 + - - +
98B MET* 3.2 45.9 + - + +
99B VAL 3.9 0.4 - - - -
100B GLU* 3.4 27.5 - - - +
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ALA 2.9 16.0 + - - -
82A ALA 3.4 3.1 + - - -
84A LYS* 1.3 76.4 - - - +
86A ARG* 1.3 59.0 + - - +
88A ASP* 3.2 10.6 + - - +
89A GLN* 3.0 42.1 + - - +
294A ARG* 3.0 31.9 + - - -
70B SER* 5.5 3.4 - - - -
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA 3.2 8.2 + - - +
83A ILE 3.8 0.2 - - - -
85A SER* 1.3 76.7 + - - +
87A ALA* 1.3 64.2 + - - +
89A GLN* 3.0 35.8 + - - +
90A LEU* 3.0 56.4 + - + +
297A GLY 3.0 27.1 - - - +
298A GLN* 3.6 24.6 + - - +
301A VAL* 3.7 19.5 - - + +
302A ASP* 2.4 37.0 + - - -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 5.3 1.6 - - + -
83A ILE 3.1 8.2 + - - +
84A LYS* 3.0 16.0 + - + +
86A ARG* 1.3 81.1 - - - +
88A ASP* 1.3 67.0 + - - +
91A GLY 3.3 2.3 + - - -
92A ALA* 3.1 45.4 + - + +
93A SER 4.7 0.7 - - - -
94A VAL* 3.2 33.9 - - + -
301A VAL* 4.7 4.0 - - - -
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Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 3.0 43.4 + - - +
85A SER* 3.4 11.0 - - - +
87A ALA* 1.3 81.7 - - - +
89A GLN* 1.3 63.6 + - + +
91A GLY* 3.5 9.4 + - - -
92A ALA 4.7 4.1 - - - +
70B SER* 4.9 0.9 + - - -
100B GLU* 3.2 28.3 - - - +
101B ARG 4.8 0.7 + - - -
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER* 3.0 28.7 + - - +
86A ARG* 3.0 40.7 + - - +
88A ASP* 1.3 76.3 - - + +
90A LEU* 1.3 63.3 + - - +
91A GLY 3.2 4.2 + - - -
294A ARG* 5.7 0.6 - - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 4.8 7.1 - - - +
86A ARG* 3.0 45.1 + - - +
87A ALA 4.6 0.2 - - - +
89A GLN* 1.3 77.0 - - - +
91A GLY* 1.3 56.2 + - - +
92A ALA* 3.3 9.3 + - + +
301A VAL* 4.7 3.8 - - + -
302A ASP* 3.4 29.4 - - - +
305A LEU* 3.8 30.0 - - + +
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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