Contacts of the helix formed by residues 87 - 97 (chain A) in PDB entry 3LBF
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 GLY 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.4 12.4 - - - -
84A THR* 2.8 10.5 + - - -
85A GLY 3.2 1.0 + - - -
86A SER* 1.3 77.7 - - - +
88A TYR* 1.3 58.6 + - - +
89A GLN 3.5 2.0 - - - -
90A THR* 3.2 21.2 - - - -
91A ALA* 2.9 25.8 + - - +
113A ALA* 3.9 12.6 - - - -
117A LEU* 3.7 6.3 - - - +
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Residues in contact with TYR 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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9A LEU* 5.2 2.1 - - - +
27A LEU* 3.2 28.5 + - + +
30A VAL* 3.7 26.5 - - + -
32A ARG* 3.1 60.3 + - + +
35A PHE* 3.4 20.6 - + + -
45A TRP* 5.3 1.0 - - - -
58A ILE* 3.5 14.6 - - + -
61A PRO* 4.7 2.8 - - + +
64A VAL* 4.1 20.0 - - + -
86A SER* 3.1 17.0 + - - +
87A GLY* 1.3 77.3 - - - +
89A GLN* 1.3 65.5 + - - +
91A ALA* 3.2 6.2 + - - +
92A ILE* 3.2 36.2 + - + +
300A SAH 3.3 6.6 + - - +
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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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64A VAL* 3.6 33.1 - - + +
67A MET* 4.7 1.6 - - - +
68A THR* 2.9 27.1 + - - -
81A GLU* 3.0 20.0 - - - +
87A GLY 3.5 0.2 - - - -
88A TYR* 1.3 75.3 - - - +
90A THR* 1.3 63.1 + - - +
92A ILE* 3.2 13.8 + - - +
93A LEU* 3.0 37.4 + - + +
146A ILE* 3.4 26.9 - - + +
148A THR* 4.5 7.6 - - + +
300A SAH 3.1 22.4 + - - +
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Residues in contact with THR 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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81A GLU* 2.7 28.2 + - - +
84A THR* 3.5 8.9 + - + +
87A GLY* 3.2 24.0 - - - -
89A GLN* 1.3 77.9 - - - +
91A ALA* 1.3 57.5 + - - +
93A LEU* 3.3 7.2 + - - +
94A ALA* 2.9 28.1 + - - +
100A VAL* 4.2 8.5 - - + +
102A SER* 4.0 9.6 - - - -
117A LEU* 3.7 11.4 - - + -
125A VAL* 3.6 31.4 - - + -
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Residues in contact with ALA 91 (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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30A VAL* 3.9 15.5 - - + -
35A PHE* 3.8 16.6 - - + -
87A GLY 2.9 12.9 + - - +
88A TYR 3.2 8.7 + - - +
90A THR* 1.3 72.6 - - - +
92A ILE* 1.3 66.6 + - - +
94A ALA* 3.2 3.0 + - - +
95A HIS* 3.1 27.4 + - - -
117A LEU* 3.8 13.7 - - + -
120A LEU* 4.5 1.6 - - + -
122A LEU* 3.9 19.0 - - + +
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Residues in contact with ILE 92 (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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26A ALA* 3.9 15.7 - - + +
27A LEU* 3.8 29.4 - - + -
30A VAL* 3.9 20.0 - - + -
64A VAL* 3.5 25.8 - - + -
68A THR* 4.5 5.8 - - + +
88A TYR* 3.2 39.0 + - + +
89A GLN* 3.2 18.1 + - - +
91A ALA* 1.3 76.5 - - - +
93A LEU* 1.3 62.9 + - - +
95A HIS* 3.1 18.4 + - - +
96A LEU* 3.5 19.4 + - + +
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Residues in contact with LEU 93 (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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68A THR* 4.1 5.4 - - + +
71A LEU* 4.0 17.0 - - + -
73A LEU* 3.7 25.6 - - + -
79A VAL* 4.2 8.3 - - + -
81A GLU* 4.0 24.7 - - + +
89A GLN* 3.0 35.6 + - + +
90A THR* 3.6 5.4 - - - +
92A ILE* 1.3 75.7 - - - +
94A ALA* 1.3 57.8 + - - +
96A LEU* 2.8 23.5 + - - +
97A VAL* 3.1 18.7 + - + +
100A VAL* 3.7 22.7 - - + -
146A ILE* 3.9 21.8 - - + -
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Residues in contact with ALA 94 (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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90A THR 2.9 16.2 + - - +
91A ALA 3.6 6.1 - - - +
92A ILE 3.2 0.6 - - - -
93A LEU* 1.3 77.4 - - - +
95A HIS* 1.3 62.3 + - - +
96A LEU 3.4 0.3 + - - -
97A VAL 3.5 3.8 - - - +
100A VAL* 3.8 5.1 - - - +
122A LEU* 4.1 17.7 - - + +
124A ASN* 2.9 42.5 + - - +
125A VAL* 3.7 19.1 - - + -
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Residues in contact with HIS 95 (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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26A ALA* 4.0 17.7 - - + -
29A ALA* 4.0 26.4 + - + +
30A VAL* 3.5 24.7 - - + +
91A ALA 3.1 22.7 + - - -
92A ILE 3.1 9.6 + - - +
94A ALA* 1.3 76.9 - - - +
96A LEU* 1.3 60.6 + - - +
120A LEU* 6.1 1.4 - - - +
122A LEU* 4.1 24.9 - - + +
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Residues in contact with LEU 96 (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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22A GLN* 3.5 43.1 - - + +
23A VAL* 4.2 9.0 - - + +
26A ALA* 3.9 8.3 - - + -
68A THR* 3.6 31.0 - - + -
73A LEU* 4.2 14.5 - - + -
74A THR 3.4 15.2 - - - +
75A PRO* 3.5 12.6 - - - +
92A ILE* 3.6 23.8 - - + +
93A LEU* 2.8 7.1 + - - +
95A HIS* 1.3 82.7 - - + +
97A VAL* 1.3 66.0 + - + +
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.8 22.0 - - + -
74A THR 3.4 16.2 - - - +
75A PRO* 3.7 4.0 - - - -
77A SER* 3.5 21.3 - - - +
79A VAL* 3.8 13.7 - - + -
93A LEU* 3.3 14.1 - - + +
94A ALA 3.5 1.9 - - - +
95A HIS 3.7 0.2 - - - -
96A LEU* 1.3 84.9 - - - +
98A GLN* 1.3 60.8 + - - +
99A HIS 3.6 13.2 - - - +
100A VAL* 3.5 23.3 - - + -
124A ASN* 2.8 24.1 + - - -
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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
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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