Contacts of the helix formed by residues 104 - 121 (chain A) in PDB entry 4YYJ
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 THR 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN* 3.5 9.3 - - + +
101A ARG* 2.6 35.6 + - + +
102A PRO 3.2 0.4 - - - -
103A ASP* 1.3 91.0 - - - +
105A VAL* 1.3 65.2 + - - +
106A TYR* 3.2 16.3 + - + -
107A TYR* 3.3 13.5 + - - +
108A LYS* 3.2 24.7 + - - +
60B ILE* 6.1 1.1 - - + -
8C BTK 6.1 1.3 - - - +
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 5.9 2.5 - - + -
44A PHE* 3.9 27.4 - - + -
104A THR* 1.3 72.4 - - - +
106A TYR* 1.3 65.4 + - + +
108A LYS* 4.0 5.5 - - - +
109A LEU* 2.9 35.9 + - + +
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 3.7 44.7 - + + -
45A PHE* 4.6 2.8 - - - -
96A ALA* 4.6 0.9 - - - +
100A ASN* 3.5 37.0 - - + +
104A THR* 3.1 13.6 - - + -
105A VAL* 1.3 83.1 - - + +
107A TYR* 1.3 57.1 + - - +
109A LEU* 3.8 3.7 - - - +
110A ALA* 2.9 31.3 + - - +
8C BTK 3.6 67.2 - - + +
9C GLY* 4.1 11.9 - - - -
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Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 4.5 6.3 - - - -
97A MET* 3.2 47.2 - - + +
100A ASN* 3.4 16.2 - - + +
101A ARG 3.2 19.3 - - - +
102A PRO* 3.5 42.3 - - + +
104A THR* 3.3 4.4 + - - +
106A TYR* 1.3 77.4 - - - +
108A LYS* 1.3 61.4 + - + +
110A ALA* 3.2 4.4 + - - +
111A LYS* 3.0 50.2 + - + +
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO 3.9 9.9 - - - +
103A ASP* 2.9 38.6 + - - +
104A THR 3.2 12.6 + - - +
105A VAL* 4.0 4.7 - - - +
107A TYR* 1.3 81.0 - - + +
109A LEU* 1.3 63.1 + - - +
111A LYS* 3.6 4.1 + - - +
112A LYS* 3.0 25.3 + - - +
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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
----------------------------------------------------------
39A LYS 3.7 20.0 - - - +
40A ASP* 3.6 31.2 - - + +
41A PRO* 5.7 2.5 - - + -
42A HIS* 6.5 0.2 - - + -
44A PHE* 4.0 17.0 - - + -
45A PHE* 3.8 20.0 - - + -
105A VAL* 2.9 22.1 + - + +
106A TYR* 3.9 3.8 - - - +
108A LYS* 1.3 75.8 - - - +
110A ALA* 1.3 58.9 + - - +
112A LYS* 3.2 16.9 + - + -
113A ILE* 2.9 36.9 + - + +
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Residues in contact with ALA 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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45A PHE* 3.6 14.5 - - + -
93A CYS* 3.7 16.4 - - - +
96A ALA* 3.5 28.5 - - + -
97A MET* 3.8 7.2 - - + -
106A TYR 2.9 19.0 + - - +
107A TYR 3.2 4.0 + - - +
109A LEU* 1.3 74.1 - - - +
111A LYS* 1.3 57.6 + - - +
113A ILE* 3.7 5.0 - - - +
114A LEU* 2.9 32.4 + - - +
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 3.7 18.6 - - - -
107A TYR* 3.0 40.2 + - + +
108A LYS* 3.9 5.6 - - - +
110A ALA* 1.3 73.1 - - - +
112A LYS* 1.3 66.1 + - - +
114A LEU* 3.4 2.4 + - - +
115A HIS* 3.2 50.6 + - + +
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Residues in contact with LYS 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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108A LYS 3.0 18.9 + - - +
109A LEU* 3.6 17.7 - - + +
111A LYS* 1.3 77.8 - - - +
113A ILE* 1.3 63.5 + - - +
115A HIS* 3.6 1.7 + - - +
116A ALA* 3.2 25.4 + - + +
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Residues in contact with ILE 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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36A LEU* 3.3 17.7 - - + +
39A LYS* 3.0 52.9 - - + +
40A ASP* 4.3 5.2 - - + +
45A PHE* 4.7 10.8 - - + -
67A PHE* 4.6 9.9 - - + -
89A PHE* 3.2 16.5 - - + -
92A MET* 5.5 0.4 - - + -
93A CYS* 3.8 15.5 - - - -
109A LEU* 2.9 26.3 + - + +
110A ALA* 3.7 9.0 - - - +
112A LYS* 1.3 76.3 - - - +
114A LEU* 1.3 64.9 + - - +
116A ALA* 4.5 4.5 - - - +
117A GLY 2.8 23.4 + - - -
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Residues in contact with LEU 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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89A PHE* 3.9 2.8 - - + -
90A LYS* 4.0 18.4 - - + -
93A CYS* 3.7 22.9 - - + -
94A ASP* 4.0 10.1 - - - +
97A MET* 3.9 26.0 - - + -
110A ALA 2.9 19.5 + - - +
111A LYS 3.8 4.0 - - - +
112A LYS 3.3 0.6 - - - -
113A ILE* 1.3 77.4 - - - +
115A HIS* 1.3 83.5 + - + +
118A PHE* 3.0 55.6 + - + -
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Residues in contact with HIS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 6.1 0.7 - - + -
111A LYS* 3.2 45.8 + - + +
112A LYS* 4.4 1.6 - - - +
114A LEU* 1.3 95.6 - - + +
116A ALA* 1.3 62.4 + - - +
118A PHE* 3.3 5.9 + - - +
119A LYS* 3.1 24.0 + - - +
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Residues in contact with ALA 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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39A LYS* 4.3 24.9 + - + +
112A LYS* 3.2 22.0 + - + +
113A ILE 4.3 1.1 - - - +
115A HIS* 1.3 73.8 - - - +
117A GLY* 1.3 61.0 + - - +
119A LYS* 3.4 10.9 + - - +
120A MET* 2.9 28.6 + - - +
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.6 25.6 - - - -
39A LYS* 4.4 3.0 - - - +
89A PHE* 3.9 2.9 - - - -
113A ILE 2.8 18.6 + - - -
116A ALA* 1.3 77.3 - - - +
118A PHE* 1.3 62.9 + - - +
120A MET* 3.1 4.5 + - - +
121A MET* 3.0 36.0 + - - +
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Residues in contact with PHE 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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86A LYS* 3.6 52.7 + - + +
87A ALA* 5.5 0.2 - - - -
89A PHE* 3.8 19.5 - + - -
90A LYS* 3.9 20.4 - - + -
114A LEU* 3.0 47.3 + - + +
115A HIS* 3.9 4.7 - - - +
117A GLY* 1.3 79.2 - - - +
119A LYS* 1.3 61.3 + - - +
121A MET* 3.3 9.1 + - + +
122A SER* 3.1 24.7 + - - -
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Residues in contact with LYS 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 HIS 3.1 13.8 + - - +
116A ALA* 3.6 13.0 - - - +
118A PHE* 1.3 76.0 - - - +
120A MET* 1.3 63.5 + - - +
122A SER* 3.4 19.3 + - - -
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Residues in contact with MET 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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32A PHE* 3.9 19.5 - - + +
35A GLN* 3.6 54.5 - - + +
36A LEU* 3.5 33.4 - - + +
39A LYS* 4.6 13.9 - - - +
116A ALA 2.9 18.2 + - - +
117A GLY* 3.1 2.0 + - - +
119A LYS* 1.3 78.4 - - - +
121A MET* 1.3 64.7 + - + +
122A SER 3.3 6.1 + - - -
31D HIS* 3.3 32.3 + - + -
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Residues in contact with MET 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.7 45.8 - - + -
36A LEU* 4.2 9.9 - - + -
82A VAL* 4.9 1.7 - - - +
85A PHE* 3.6 31.4 - - + -
86A LYS* 3.4 44.7 + - + -
89A PHE* 3.7 30.1 - - + -
117A GLY 3.0 23.7 + - - +
118A PHE* 3.3 6.9 + - + +
120A MET* 1.3 81.0 - - + +
122A SER* 1.3 59.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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