Contacts of the helix formed by residues 78 - 88 (chain A) in PDB entry 4BLV
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 LEU 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A THR* 3.5 41.7 - - + +
68A ILE* 4.5 5.4 - - + -
74A LEU* 3.8 18.2 - - + -
75A PRO* 2.9 13.7 + - + +
77A GLU* 1.3 80.8 - - + +
79A GLU* 1.3 60.4 + - - +
80A ALA 3.5 2.0 - - - -
81A TYR* 3.4 11.4 + - + +
82A ILE* 2.9 32.2 + - + +
256A VAL* 3.7 30.3 - - + -
259A TRP* 3.7 28.5 - - + -
260A LEU* 4.0 13.5 - - + -
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Residues in contact with GLU 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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74A LEU* 4.1 22.4 - - + +
75A PRO 4.0 3.4 - - - +
76A ALA* 3.3 36.4 + - + +
77A GLU 3.5 0.2 - - - -
78A LEU* 1.3 78.1 - - - +
80A ALA* 1.3 58.8 + - - +
83A ASN* 2.8 51.0 + - - +
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Residues in contact with ALA 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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23A SER* 4.8 4.3 - - - +
27A GLU* 4.1 32.5 - - + +
76A ALA 5.0 0.6 + - - -
77A GLU 5.1 3.7 + - - +
78A LEU 3.5 0.6 - - - -
79A GLU* 1.3 77.6 - - - +
81A TYR* 1.3 63.6 + - - +
83A ASN* 4.0 5.9 - - - +
84A VAL* 3.3 26.2 + - - +
107A LEU* 4.1 17.7 - - + +
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Residues in contact with TYR 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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16A VAL* 3.5 18.8 - - - +
19A HIS* 3.5 24.5 - - + -
20A THR* 3.8 24.7 - - - -
23A SER* 3.7 24.6 + - - +
65A ILE* 3.6 12.8 - - + +
68A ILE* 4.4 10.5 - - + -
77A GLU 5.5 0.2 + - - -
78A LEU* 3.4 14.0 + - + +
79A GLU 3.3 0.2 - - - -
80A ALA* 1.3 78.9 - - - +
82A ILE* 1.3 78.9 + - + +
84A VAL* 3.0 17.9 + - - +
85A VAL* 3.2 23.0 + - + +
97A TYR* 2.7 35.1 + - - -
103A ILE* 4.2 14.8 - - + -
107A LEU* 5.5 0.7 - - - -
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Residues in contact with ILE 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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65A ILE* 3.8 29.4 - - + -
68A ILE* 4.0 10.1 - - + -
69A TRP* 3.6 32.3 - - + +
74A LEU* 3.8 34.8 - - + -
78A LEU* 2.9 26.4 + - + +
79A GLU* 4.1 1.1 - - - +
81A TYR* 1.3 88.0 - - + +
83A ASN* 1.3 59.3 + - - +
85A VAL* 3.1 4.8 + - + +
86A LYS* 2.8 41.8 + - + +
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Residues in contact with ASN 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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79A GLU* 2.8 41.1 + - - +
80A ALA* 4.0 5.7 - - - +
82A ILE* 1.3 74.9 - - - +
84A VAL* 1.3 60.5 + - - +
86A LYS* 3.9 22.9 + - - +
87A HIS* 3.1 22.2 + - - +
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Residues in contact with VAL 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 ALA 3.3 15.5 + - - +
81A TYR* 3.0 11.8 + - - +
83A ASN* 1.3 75.3 - - - +
85A VAL* 1.3 65.6 + - - +
87A HIS* 3.1 14.5 + - - +
88A PHE* 3.2 40.2 - - + -
98A PRO* 4.0 5.4 - - + -
102A LEU 4.2 0.4 - - - -
103A ILE* 4.0 33.9 - - + +
106A LEU* 4.1 21.3 - - + -
107A LEU* 3.9 24.2 - - + -
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Residues in contact with VAL 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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65A ILE* 4.1 24.2 - - + -
69A TRP* 3.9 20.9 - - + -
81A TYR* 3.2 34.4 + - + +
82A ILE* 3.1 12.2 + - + +
84A VAL* 1.3 75.7 - - - +
86A LYS* 1.3 61.6 + - - +
88A PHE* 3.2 5.9 + - - +
89A ASN* 2.8 36.7 + - - +
94A LEU* 4.3 4.7 - - + -
96A TYR 4.9 0.2 - - - +
97A TYR* 4.1 11.0 - - + -
98A PRO* 4.0 23.3 - - + -
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Residues in contact with LYS 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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69A TRP* 3.7 44.3 + - + -
70A GLN* 5.3 6.1 - - - +
74A LEU* 6.1 1.4 - - - +
82A ILE* 2.8 23.2 + - + +
83A ASN* 3.9 24.4 + - - +
84A VAL 3.2 0.2 - - - -
85A VAL* 1.3 73.4 - - - +
87A HIS* 1.3 66.1 + - - +
89A ASN 2.9 22.7 + - - +
90A ARG* 3.3 7.8 + - - +
110B GLU* 5.0 13.7 - - - +
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Residues in contact with HIS 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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83A ASN 3.1 15.2 + - - +
84A VAL 3.1 9.8 + - - +
86A LYS* 1.3 76.5 - - - +
88A PHE* 1.3 74.8 + + - +
89A ASN 3.3 0.2 - - - -
90A ARG* 3.0 63.6 + - - +
106A LEU* 3.5 25.8 - - + -
1298A SO4 2.9 30.9 + - - -
87B HIS* 3.2 31.5 + + - -
90B ARG* 5.9 0.2 + - - -
105B ARG* 4.3 8.9 + - - -
106B LEU* 4.8 3.1 - - + -
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Residues in contact with PHE 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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47A ARG* 3.6 39.0 + - + +
84A VAL* 3.2 37.6 + - + -
85A VAL 3.2 7.5 + - - +
86A LYS 3.1 0.8 - - - -
87A HIS* 1.3 92.9 - + - +
89A ASN* 1.3 71.9 + - - +
90A ARG 3.8 1.3 - - - -
96A TYR* 3.8 23.8 - - + +
98A PRO* 3.7 27.4 - - + -
102A LEU* 3.9 21.5 - - + -
105A ARG* 5.9 0.2 - - - -
106A LEU* 3.9 15.0 - - + -
1298A SO4 3.6 23.6 - - - -
105B ARG* 6.0 0.9 - - - +
133B LYS* 5.0 6.4 - - - +
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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
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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