Contacts of the helix formed by residues 77 - 94 (chain A) in PDB entry 3DBD
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 LYS 77 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU 3.3 5.8 - - - +
76A LEU* 1.3 78.1 - - - +
78A PRO* 1.3 76.1 - - + +
79A HIS* 3.1 37.7 - - + +
80A GLN* 3.2 34.1 + - + +
81A LYS 3.2 8.0 + - - -
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Residues in contact with PRO 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU 3.7 6.7 - - - +
77A LYS* 1.3 91.6 - - + +
79A HIS* 1.3 59.0 + - - +
81A LYS* 3.3 11.6 + - + +
82A GLU* 3.2 19.9 + - - +
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Residues in contact with HIS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 3.1 33.1 - - + -
78A PRO* 1.3 81.0 - - - +
80A GLN* 1.3 77.2 + - + +
82A GLU* 3.3 26.0 + - - +
83A LYS* 3.7 37.1 + - + +
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Residues in contact with GLN 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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74A MET 3.0 21.2 + - - +
75A LEU* 3.7 23.4 - - + +
76A LEU* 4.0 1.2 + - - +
77A LYS* 3.2 37.1 + - + +
79A HIS* 1.3 89.5 - - + +
81A LYS* 1.3 61.4 + - - +
82A GLU 3.1 2.5 + - - -
83A LYS* 3.5 15.2 + - - +
84A MET* 3.8 8.1 + - - +
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.4 21.3 - - + +
77A LYS 3.2 9.4 + - - +
78A PRO* 3.5 15.7 - - + +
79A HIS 3.2 0.8 - - - -
80A GLN* 1.3 76.8 - - - +
82A GLU* 1.3 59.7 + - - +
84A MET* 4.1 9.0 + - + +
85A SER* 3.1 23.4 + - - -
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Residues in contact with GLU 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 PRO 3.2 10.3 + - - +
79A HIS* 3.4 19.8 + - - +
80A GLN 3.1 0.8 - - - -
81A LYS* 1.3 76.7 - - - +
83A LYS* 1.3 74.4 + - - +
84A MET 3.2 0.2 - - - -
85A SER* 2.7 18.5 + - - +
86A THR* 2.7 37.3 + - - +
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.9 35.8 - - + +
80A GLN* 3.5 10.4 + - - +
82A GLU* 1.3 94.4 + - - +
84A MET* 1.3 57.0 + - - +
86A THR* 3.6 8.0 + - - +
87A GLU* 3.1 27.8 + - - +
182A GLY* 4.9 14.9 - - - +
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Residues in contact with MET 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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70A VAL* 4.6 15.5 - - + -
75A LEU* 4.2 28.0 - - + -
80A GLN 3.8 11.3 + - - +
81A LYS* 4.4 7.9 - - + +
82A GLU 3.2 0.6 - - - -
83A LYS* 1.3 77.5 - - - +
85A SER* 1.3 62.1 + - - +
87A GLU* 3.4 13.8 + - - +
88A ILE* 3.0 51.0 + - + +
105A PHE* 5.8 1.6 - - + -
107A GLU* 5.9 0.9 - - - +
112A VAL* 3.7 40.2 - - + -
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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 LYS 3.1 15.9 + - - -
82A GLU* 2.7 24.3 + - - +
84A MET* 1.3 79.3 - - - +
86A THR* 1.3 58.4 + - - +
88A ILE* 4.0 9.7 - - - +
89A ALA* 3.2 27.4 + - - +
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Residues in contact with THR 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 GLU* 2.7 36.1 + - - +
83A LYS* 3.8 8.8 - - - +
84A MET 3.2 0.2 - - - -
85A SER* 1.3 76.8 + - - +
87A GLU* 1.3 64.3 + - - +
89A ALA* 3.5 5.5 + - + +
90A ILE* 3.2 39.8 + - + +
184A ALA 4.9 5.4 - - - +
185A THR* 6.1 0.7 - - - -
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Residues in contact with GLU 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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68A LYS* 4.3 12.6 + - - -
83A LYS 3.1 18.5 + - - +
84A MET* 3.4 14.8 + - - +
86A THR* 1.3 74.5 - - - +
88A ILE* 1.3 61.7 + - + +
90A ILE* 3.4 5.8 + - - +
91A HIS* 2.9 38.4 + - + +
180A ASP* 4.2 8.1 - - - +
181A PHE* 3.3 46.0 + - + +
182A GLY* 3.4 18.3 + - - -
184A ALA 6.0 0.2 - - - -
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Residues in contact with ILE 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 MET* 3.0 43.7 + - + +
85A SER* 4.0 7.4 - - - +
87A GLU* 1.3 78.8 - - + +
89A ALA* 1.3 57.7 + - - +
91A HIS* 4.5 0.2 - - - -
92A LYS* 2.7 42.0 + - + +
102A PHE* 3.7 27.5 - - + -
105A PHE* 3.6 57.4 - - + -
112A VAL* 5.3 0.2 - - + -
114A VAL* 4.3 13.5 - - + -
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Residues in contact with ALA 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 3.2 17.5 + - - +
86A THR* 3.8 7.6 - - + +
87A GLU 3.4 0.2 - - - -
88A ILE* 1.3 80.6 - - - +
90A ILE* 1.3 62.4 + - + +
92A LYS* 4.3 4.9 - - - +
93A SER* 3.5 19.2 + - - -
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Residues in contact with ILE 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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86A THR* 3.2 29.4 + - + +
87A GLU* 3.8 4.9 - - - +
88A ILE 3.2 0.2 - - - -
89A ALA* 1.3 76.6 - - + +
91A HIS* 1.3 63.6 + - - +
93A SER* 2.7 22.4 + - - -
94A LEU* 3.3 16.5 - - + +
158A VAL* 3.8 33.0 - - + -
181A PHE* 4.5 4.3 - - + -
184A ALA* 3.4 41.5 - - + +
185A THR* 4.0 11.9 - - - -
186A LYS* 4.3 17.0 - - + +
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Residues in contact with HIS 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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87A GLU* 2.9 23.6 + - + +
88A ILE 3.9 0.9 - - - +
90A ILE* 1.3 77.3 - - - +
92A LYS* 1.3 61.1 - - - +
94A LEU* 3.1 26.0 + - + +
100A VAL* 2.6 40.5 + - + -
102A PHE* 3.4 33.8 + + + +
116A LEU* 3.7 22.7 - - + +
179A GLY* 4.7 4.0 - - - -
180A ASP 4.8 2.7 - - - -
181A PHE* 3.2 39.8 + + + +
313A 3FR 5.9 0.4 - - + -
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Residues in contact with LYS 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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88A ILE* 2.7 27.6 + - + +
89A ALA* 4.3 5.4 - - - +
91A HIS* 1.3 74.4 - - - +
93A SER* 1.3 60.7 + - - +
94A LEU 3.4 5.2 + - - +
102A PHE* 3.7 36.3 - - + +
104A GLY* 5.9 0.7 - - - -
105A PHE* 6.1 1.3 - - + -
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Residues in contact with SER 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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89A ALA 3.5 12.3 + - - -
90A ILE* 2.7 23.4 + - - +
92A LYS* 1.3 77.8 - - - +
94A LEU* 1.3 68.5 + - - +
95A ASP* 3.7 4.0 + - - +
152A TYR* 4.0 4.0 + - - -
156A ASN* 5.6 2.4 + - - -
186A LYS* 6.0 2.3 - - - +
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Residues in contact with LEU 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 ILE* 3.3 24.5 - - + +
91A HIS* 3.1 23.6 + - + +
92A LYS 4.0 4.5 - - - +
93A SER* 1.3 87.4 + - - +
95A ASP* 1.3 62.4 + - - +
99A VAL* 4.0 14.4 - - + -
100A VAL 5.6 0.7 - - - +
101A GLY* 5.6 1.4 - - - -
102A PHE* 4.9 9.7 + - - +
152A TYR* 3.5 24.2 - - + +
153A LEU* 3.8 9.6 - - + -
156A ASN* 5.4 6.7 - - + +
158A VAL* 4.4 20.0 - - + -
181A PHE* 3.6 38.1 - - + -
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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