Contacts of the helix formed by residues 102 - 120 (chain A) in PDB entry 4BHT
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 ASN 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLU* 4.8 4.6 + - - -
80A TRP* 3.8 14.6 - - + -
100A SER 3.4 8.1 + - - +
101A VAL* 1.3 76.2 - - - +
103A LEU* 1.3 64.7 + - - +
104A SER* 3.3 11.3 + - - -
105A ILE* 2.9 48.8 + - - +
106A LEU* 3.1 24.5 + - - +
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Residues in contact with LEU 103 (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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21A GLN* 3.7 22.2 - - - +
60A VAL* 3.8 33.0 - - + -
62A GLN* 5.8 3.8 - - + +
80A TRP* 3.8 28.4 - - + +
82A VAL* 3.8 10.1 - - + -
102A ASN* 1.3 74.9 - - - +
104A SER* 1.3 53.5 + - - +
106A LEU* 3.2 3.3 + - - -
107A LYS* 2.7 60.2 + - + +
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Residues in contact with SER 104 (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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20A ASN 4.9 1.3 - - - -
21A GLN* 3.2 42.8 - - - +
22A THR 4.4 0.2 - - - -
23A GLU* 2.6 38.7 + - - -
24A PHE* 3.4 6.6 + - - +
102A ASN* 3.3 10.8 + - - -
103A LEU* 1.3 78.8 - - - +
105A ILE* 1.3 58.6 + - - +
107A LYS* 3.3 2.8 + - - +
108A PHE* 2.9 28.8 + - - +
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Residues in contact with ILE 105 (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 GLU* 3.5 33.4 - - + +
96A ARG* 4.3 15.9 - - - +
100A SER* 3.3 36.6 - - - +
101A VAL* 5.1 3.1 - - - -
102A ASN* 2.9 26.3 + - - +
104A SER* 1.3 75.5 - - - +
106A LEU* 1.3 62.0 + - + +
108A PHE* 3.1 12.4 + - + +
109A LEU* 2.9 47.0 + - + +
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Residues in contact with LEU 106 (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 TRP* 3.4 50.7 - - + -
82A VAL* 4.0 15.9 - - + +
96A ARG* 4.8 8.3 - - + -
101A VAL* 3.8 18.8 - - + -
102A ASN 3.1 16.3 + - - +
103A LEU* 3.7 4.5 - - - +
105A ILE* 1.3 75.3 - - + +
107A LYS* 1.3 59.0 + - - +
109A LEU* 3.3 7.6 + - + +
110A GLY* 2.8 26.5 + - - -
128A LYS* 3.6 20.4 - - + +
129A GLY* 3.5 25.6 - - - +
130A GLY* 4.0 9.2 - - - +
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Residues in contact with LYS 107 (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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18A ASP* 2.8 31.5 + - - -
21A GLN* 3.0 27.1 + - - +
24A PHE* 3.6 34.9 - - + -
55A VAL 5.0 0.4 + - - -
56A GLU* 5.2 3.8 + - - -
57A PRO* 4.3 26.0 - - + +
60A VAL* 5.2 1.6 - - + -
82A VAL* 4.3 12.8 - - + -
84A PHE* 3.7 9.2 - - + -
103A LEU* 2.7 41.1 + - + +
104A SER 3.7 2.5 - - - +
106A LEU* 1.3 69.2 - - - +
108A PHE* 1.3 67.1 + - - +
110A GLY 4.4 0.2 - - - +
111A PHE* 2.9 27.4 + - - +
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Residues in contact with PHE 108 (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 GLU* 3.9 36.6 - - + +
24A PHE* 3.9 8.4 - - - +
27A ALA* 3.6 22.9 - - + +
96A ARG* 6.0 1.1 - - - -
104A SER 2.9 14.5 + - - +
105A ILE* 3.4 21.8 - - + +
107A LYS* 1.3 77.8 - - - +
109A LEU* 1.3 82.8 + - + +
111A PHE* 3.7 2.6 - - - +
112A GLU* 3.3 44.7 + - + +
324A GLN* 4.6 9.9 - - - -
348A ASN* 4.8 4.0 - - - -
349A MET* 3.3 30.5 - - + -
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Residues in contact with LEU 109 (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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96A ARG* 3.4 41.7 - - - +
105A ILE* 2.9 29.1 + - + +
106A LEU* 3.8 2.9 - - + +
107A LYS 3.2 0.2 - - - -
108A PHE* 1.3 104.3 - - + +
110A GLY* 1.3 56.4 + - - +
112A GLU* 3.4 10.2 + - - +
113A GLN* 3.0 32.4 + - - +
128A LYS* 3.6 34.3 - - + +
348A ASN* 4.2 17.3 - - - +
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Residues in contact with GLY 110 (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 VAL* 5.0 1.1 - - - -
84A PHE* 4.0 13.9 - - - +
106A LEU 2.8 19.5 + - - -
107A LYS 3.9 0.7 - - - -
109A LEU* 1.3 69.6 - - - +
111A PHE* 1.3 66.4 + - - +
113A GLN* 3.4 5.8 - - - +
114A THR* 2.9 27.9 + - - -
126A GLY 4.4 1.0 - - - -
127A GLY* 4.1 8.7 - - - -
128A LYS* 3.6 15.8 - - - +
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Residues in contact with PHE 111 (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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24A PHE* 4.1 6.3 - + + -
27A ALA* 4.0 24.9 - - + -
28A VAL* 4.0 13.5 - - + -
31A VAL* 3.8 33.4 - - + -
32A MET* 4.6 4.3 - - + -
54A LEU* 3.9 18.2 - - + -
55A VAL* 4.2 23.1 - - + -
84A PHE* 3.7 31.0 - + + -
107A LYS 2.9 19.3 + - - +
108A PHE* 3.7 3.8 - - - +
110A GLY* 1.3 76.8 - - - +
112A GLU* 1.3 63.2 + - + +
114A THR* 3.3 10.8 + - + -
115A PHE* 3.2 47.7 - + - -
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Residues in contact with GLU 112 (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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27A ALA* 5.2 5.8 - - + +
31A VAL* 6.4 1.6 - - + -
108A PHE* 3.3 39.0 + - + +
109A LEU* 3.8 11.5 - - - +
111A PHE* 1.3 80.3 - - + +
113A GLN* 1.3 66.0 + - - +
115A PHE* 3.1 10.5 + - - +
116A LYS* 2.9 30.8 + - + +
348A ASN* 3.4 19.1 - - - +
349A MET* 3.7 14.3 - - - +
370A LYS* 3.8 35.2 + - + +
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Residues in contact with GLN 113 (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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92A LYS 3.4 22.9 - - - +
93A GLY* 3.9 9.1 - - - -
94A GLY 5.3 0.2 - - - -
109A LEU* 3.0 19.0 + - - +
110A GLY 3.2 6.0 + - - +
112A GLU* 1.3 78.6 - - - +
114A THR* 1.3 54.9 + - - +
116A LYS* 4.3 22.0 + - - +
117A ASN* 2.8 58.8 + - - +
126A GLY* 4.4 0.2 - - - -
127A GLY 3.7 14.4 - - - +
128A LYS* 4.0 17.7 + - + -
377A VAL* 3.8 18.4 - - - +
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Residues in contact with THR 114 (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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54A LEU* 5.2 2.9 - - + -
84A PHE* 3.8 15.8 - - + +
85A SER* 3.6 24.6 - - - +
110A GLY 2.9 13.5 + - - -
111A PHE* 3.4 13.5 - - + -
113A GLN* 1.3 76.6 - - - +
115A PHE* 1.3 64.5 + - + +
117A ASN* 4.1 1.6 - - - +
118A ALA* 3.2 26.7 + - - +
124A MET 5.0 1.4 - - - +
125A GLY* 4.6 1.9 - - - +
126A GLY* 3.3 23.3 - - - +
437A VAL* 3.9 22.7 - - + +
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Residues in contact with PHE 115 (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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31A VAL* 4.5 21.8 - - + -
54A LEU* 3.7 39.0 - - + -
111A PHE* 3.2 57.0 - + - -
112A GLU* 3.1 8.3 + - - +
114A THR* 1.3 78.8 - - + +
116A LYS* 1.3 59.9 + - - +
118A ALA* 3.3 4.6 + - - +
119A LEU* 3.0 32.8 + - + +
430A ASN* 5.2 6.7 - - - +
433A GLY* 3.7 27.9 - - - -
434A PHE* 3.9 17.9 - + + -
437A VAL* 4.1 10.3 - - + -
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Residues in contact with LYS 116 (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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112A GLU* 2.9 22.9 + - + +
113A GLN* 3.8 22.4 + - - +
115A PHE* 1.3 74.1 - - - +
117A ASN* 1.3 64.7 + - - +
119A LEU* 3.2 16.1 + - - +
120A THR* 3.3 15.1 - - - +
348A ASN* 5.6 6.1 + - - +
369A GLY 4.5 0.8 - - - +
370A LYS* 3.6 34.1 - - + +
373A ASN* 2.7 36.5 + - - +
374A ALA* 4.1 20.9 - - + +
377A VAL* 4.2 15.0 - - + +
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Residues in contact with ASN 117 (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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92A LYS* 3.1 28.0 + - - +
113A GLN* 2.8 28.2 + - - +
114A THR 4.1 1.6 - - - +
116A LYS* 1.3 71.6 - - - +
118A ALA* 1.3 62.5 + - - +
120A THR* 2.8 28.9 + - - -
122A LEU 4.0 7.1 - - - +
124A MET* 3.7 22.6 - - + +
125A GLY 2.5 30.9 + - - +
377A VAL* 2.9 32.1 - - - +
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Residues in contact with ALA 118 (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* 3.6 19.1 - - + -
114A THR 3.2 17.9 + - - +
115A PHE 3.6 5.4 - - - +
116A LYS 3.2 0.2 - - - -
117A ASN* 1.3 78.1 - - - +
119A LEU* 1.3 63.1 + - - +
120A THR 3.2 0.7 + - - -
121A THR* 3.2 13.7 + - - +
122A LEU 5.3 2.2 - - - -
124A MET 4.5 2.0 + - - -
433A GLY* 3.7 10.3 - - - +
436A LYS* 4.1 18.2 + - + +
437A VAL* 3.5 23.3 - - + -
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Residues in contact with LEU 119 (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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115A PHE 3.0 15.8 + - - +
116A LYS* 3.4 9.6 - - - +
117A ASN 3.2 0.2 - - - -
118A ALA* 1.3 78.1 - - - +
120A THR* 1.3 61.3 + - - +
121A THR* 3.0 9.2 + - - +
370A LYS* 3.7 22.7 - - + +
371A ALA* 4.2 1.3 - - - -
374A ALA* 5.9 0.9 - - + -
409A ILE* 3.3 45.0 - - + +
412A ALA* 4.2 12.0 - - + +
413A CYS* 4.9 0.9 - - - -
429A ALA* 4.0 26.5 - - + +
432A ALA* 3.8 31.4 - - + -
433A GLY* 4.1 10.1 - - - +
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Residues in contact with THR 120 (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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116A LYS 3.3 16.2 - - - +
117A ASN* 2.8 18.8 + - - +
118A ALA 3.2 0.2 - - - -
119A LEU* 1.3 76.4 - - - +
121A THR* 1.3 71.4 + - - +
122A LEU* 3.0 32.1 + - - +
124A MET* 3.8 4.2 - - + +
374A ALA* 4.4 3.4 - - + +
377A VAL* 3.9 23.8 - - + -
378A ALA* 4.2 15.3 - - + -
405A ILE* 3.4 21.3 - - - +
409A ILE* 4.0 15.3 - - + -
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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