Contacts of the helix formed by residues 106 - 125 (chain B) in PDB entry 2XGZ
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 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU 3.7 5.6 - - - -
48B MET* 3.9 12.1 - - - +
102B LYS* 2.8 16.2 + - - -
103B SER 4.2 1.9 - - - -
104B LYS 3.6 1.0 - - - -
105B LEU* 1.3 80.6 - - - +
107B ALA* 1.3 65.7 + - - -
108B ASN* 3.1 14.4 - - - -
109B ALA 3.2 2.1 + - - -
110B ILE* 3.1 23.2 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 5.5 0.4 - - - -
45B ALA* 3.7 27.1 - - + +
46B LEU 2.9 28.8 + - - +
47B GLU* 3.9 2.9 - - + +
102B LYS* 3.3 16.6 + - + -
106B GLY* 1.3 71.2 - - - -
108B ASN* 1.3 56.6 + - - +
110B ILE* 4.5 0.7 - - - -
111B LEU* 2.8 34.5 + - - +
347B ASN* 4.3 11.9 - - - +
350B GLY* 4.2 3.4 - - - +
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Residues in contact with ASN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 5.4 2.2 + - - +
19B VAL* 3.7 22.4 - - + +
34B VAL* 3.4 31.5 - - + +
47B GLU* 3.5 26.2 + - + +
48B MET 3.0 40.4 + - - +
49B ARG* 5.3 0.2 - - - +
61B VAL* 3.9 10.1 - - - +
64B ALA* 3.6 16.6 - - - +
106B GLY* 3.5 6.4 - - - -
107B ALA* 1.3 72.1 - - - +
109B ALA* 1.3 67.2 + - - +
112B GLY* 3.3 17.7 + - - -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 4.7 3.6 - - - -
21B VAL* 4.6 0.2 - - - +
64B ALA* 3.7 22.9 - - + +
67B ASN* 4.5 1.3 - - + -
68B VAL* 3.7 18.9 - - + +
72B ILE* 4.0 12.5 - - + +
105B LEU 3.5 18.2 - - - +
106B GLY 3.2 8.7 + - - +
108B ASN* 1.3 83.3 + - - +
110B ILE* 1.3 65.1 + - - +
112B GLY* 3.7 1.0 + - - -
113B VAL* 3.6 23.7 + - - +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 4.6 6.1 - - + -
93B LEU* 3.8 26.4 - - + +
94B ILE* 5.4 0.4 - - - +
97B ASP* 3.7 32.8 - - + +
102B LYS* 3.8 26.5 - - + -
105B LEU* 4.3 16.2 - - + -
106B GLY 3.1 17.4 + - - +
107B ALA* 3.9 4.5 - - - +
109B ALA* 1.3 75.4 - - - +
111B LEU* 1.3 64.6 + - - +
113B VAL* 3.2 6.6 + - - +
114B SER* 3.0 19.4 + - - -
350B GLY 3.4 16.4 - - - +
351B THR* 3.7 17.9 - - + -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 3.9 14.1 - - + -
35B PRO* 4.6 2.7 - - + -
107B ALA 2.8 22.6 + - - +
108B ASN 4.4 2.0 - - - +
110B ILE* 1.3 73.2 - - - +
112B GLY* 1.3 63.9 + - - +
114B SER* 3.1 3.5 + - - -
115B LEU* 2.9 55.5 + - + +
346B VAL* 4.0 18.4 - - + +
347B ASN* 3.3 39.5 - - + +
350B GLY* 3.3 27.1 + - - +
351B THR* 4.0 11.0 - - - +
352B LEU 4.4 0.2 - - - +
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 3.7 24.0 - - - +
32B SER* 3.5 11.7 - - - -
34B VAL* 3.6 18.9 - - - +
108B ASN 3.3 9.2 + - - -
110B ILE 3.2 1.0 - - - -
111B LEU* 1.3 77.7 - - - +
113B VAL* 1.3 60.2 + - - +
116B ALA* 3.1 26.3 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.1 12.1 - - + -
21B VAL* 4.0 18.6 - - + -
23B LEU* 4.4 8.4 - - + +
68B VAL* 4.2 7.4 - - + -
72B ILE* 4.0 20.4 - - + -
76B PHE* 3.8 35.0 - - + -
89B VAL* 5.1 0.2 - - + -
93B LEU* 3.8 14.4 - - + -
109B ALA 3.6 15.0 + - - +
110B ILE 3.2 7.0 + - - +
112B GLY* 1.3 72.1 - - - +
114B SER* 1.3 66.5 + - - +
116B ALA* 3.4 1.9 + - - +
117B ALA* 3.1 23.6 + - - +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 3.1 23.8 + - - +
89B VAL* 4.4 2.5 - - - -
90B ASP* 2.6 28.3 + - - -
93B LEU* 3.7 7.0 - - - +
110B ILE 3.0 13.4 + - - -
111B LEU* 3.4 14.1 - - - -
113B VAL* 1.3 77.9 - - - +
115B LEU* 1.3 62.3 + - - +
117B ALA* 3.5 1.7 + - - +
118B SER* 3.4 10.9 + - - -
351B THR* 4.1 4.9 - - - -
352B LEU* 3.0 25.6 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B SER* 3.2 26.9 - - - +
33B ILE 5.1 6.7 - - - +
34B VAL* 5.6 1.6 - - + -
35B PRO* 5.8 1.8 - - + -
111B LEU* 2.9 47.8 + - + +
114B SER* 1.3 72.5 - - - +
116B ALA* 1.3 63.3 + - - +
117B ALA 3.2 1.6 - - - -
118B SER* 2.8 22.3 + - - -
119B ARG* 3.3 12.0 + - - +
346B VAL* 4.8 8.5 - - + -
352B LEU* 4.1 17.7 - - + -
380B ASP* 5.8 0.2 - - - +
382B PHE* 3.6 51.8 - - + -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 4.2 11.7 - - + +
23B LEU* 3.9 15.9 - - + -
30B PHE* 3.7 25.8 - - - +
31B ARG 4.8 0.4 - - - -
32B SER* 3.7 13.6 - - - +
112B GLY 3.1 19.0 + - - +
113B VAL 3.4 2.7 + - - +
115B LEU* 1.3 75.5 - - - +
117B ALA* 1.3 62.4 + - - +
119B ARG* 3.2 9.6 + - - +
120B ALA* 3.0 22.2 + - - +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 4.0 18.1 - - + +
76B PHE* 4.8 0.9 - - + -
83B VAL* 3.7 11.2 - - + +
86B GLN* 4.3 3.1 - - - +
89B VAL* 3.9 30.3 - - + -
113B VAL 3.1 18.0 + - - +
114B SER 3.6 6.1 - - - +
116B ALA* 1.3 76.5 - - - +
118B SER* 1.3 58.0 + - - +
120B ALA* 3.2 7.0 + - - +
121B ALA* 2.8 28.6 + - - +
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLN* 3.4 19.2 + - - -
114B SER 3.4 3.7 + - - -
115B LEU 2.8 19.2 + - - -
117B ALA* 1.3 78.3 - - - +
119B ARG* 1.3 56.0 + - - +
121B ALA* 3.4 6.0 + - - -
122B ALA* 2.9 26.7 + - - +
129B LEU* 3.8 3.6 - - - +
132B HIS* 3.4 18.8 - - - -
133B LEU* 4.3 3.6 - - - -
352B LEU* 3.6 17.8 - - - +
382B PHE* 3.3 22.3 - - - -
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.9 17.4 - - + -
31B ARG 2.8 39.8 + - - +
32B SER* 3.7 7.5 + - - +
115B LEU 3.3 10.7 + - - +
116B ALA 3.2 9.0 + - - +
118B SER* 1.3 76.4 + - - +
120B ALA* 1.3 64.5 + - - +
122B ALA* 3.3 4.9 + - - +
123B ALA* 3.1 22.5 + - - +
129B LEU* 3.8 29.0 - - + +
380B ASP* 2.9 40.0 + - - -
381B THR* 4.1 10.5 + - - +
382B PHE* 3.5 29.4 - - + +
385B ASP* 5.5 0.4 + - - -
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.7 25.1 - - + -
25B THR* 4.0 12.7 + - + +
27B LYS* 5.1 1.7 - - - +
30B PHE* 3.6 31.2 - - + -
83B VAL* 4.1 7.8 - - + +
116B ALA 3.0 8.4 + - - +
117B ALA 3.5 7.0 - - - +
119B ARG* 1.3 75.6 - - - +
121B ALA* 1.3 57.2 + - - +
123B ALA* 3.3 4.3 + - - +
124B GLU* 3.0 27.5 + - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 3.4 31.6 - - - +
84B LYS* 3.8 7.7 - - - +
117B ALA 2.8 17.6 + - - +
118B SER* 3.5 2.0 - - - +
119B ARG 3.2 0.2 - - - -
120B ALA* 1.3 73.2 - - - +
122B ALA* 1.3 64.5 + - - +
124B GLU* 3.1 7.6 + - - +
125B LYS* 3.0 27.5 + - - +
132B HIS* 3.4 24.5 - - + +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B SER 2.9 16.3 + - - +
119B ARG* 3.3 6.3 + - - +
121B ALA* 1.3 73.7 - - - +
123B ALA* 1.3 62.4 + - - +
125B LYS* 3.3 2.8 + - - +
126B ASN 3.1 3.6 + - - -
127B VAL* 3.0 45.5 + - - +
129B LEU* 3.9 18.2 - - + +
132B HIS* 3.9 25.4 - - + -
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS* 3.4 24.8 + - + -
30B PHE* 3.4 42.0 - - + -
119B ARG 3.1 7.0 + - - +
120B ALA 3.6 3.1 - - - +
122B ALA* 1.3 73.0 - - - +
124B GLU* 1.3 65.5 + - - +
126B ASN* 3.0 14.6 + - - +
127B VAL 5.0 1.1 - - - -
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ALA 5.1 5.2 + - - -
26B GLU* 4.4 16.8 - - - +
27B LYS* 4.0 19.5 + - + +
82B ASP* 4.3 2.3 - - - +
83B VAL* 3.9 19.9 - - - +
84B LYS* 2.7 39.5 + - + +
120B ALA 3.0 13.1 + - - +
121B ALA 3.1 9.2 + - - +
123B ALA* 1.3 76.1 - - - +
125B LYS* 1.3 59.6 - - - +
126B ASN* 3.2 2.3 + - - +
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LYS* 3.9 26.7 - - + +
121B ALA 3.0 15.7 + - - +
122B ALA 3.7 4.9 - - - +
123B ALA 3.2 0.4 - - - -
124B GLU* 1.3 74.3 - - - +
126B ASN* 1.3 69.1 + - - +
127B VAL* 3.4 23.1 + - + +
132B HIS* 2.9 37.9 + - + +
135B ASP* 2.8 36.5 + - - +
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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
------------------------------------------------------------
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