Contacts of the helix formed by residues 93 - 111 (chain g) in PDB entry 3J9X
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 93 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64e THR* 4.6 0.7 - - - -
92g SER* 1.3 75.9 - - - +
94g PRO* 1.3 68.9 - - - -
95g ALA 3.3 1.8 - - - -
96g LEU* 2.7 30.2 + - - +
97g VAL* 3.1 15.5 + - - +
133g VAL* 4.3 19.3 - - - +
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Residues in contact with PRO 94 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64e THR* 3.3 17.9 - - + +
65e GLN* 3.4 27.6 - - + +
66e TYR 4.6 0.4 - - - -
67e GLY* 3.8 10.8 - - - +
92g SER 4.6 0.4 - - - +
93g GLY* 1.3 82.5 - - - -
95g ALA* 1.3 63.3 + - - +
97g VAL* 3.0 12.7 + - + +
98g ASN* 2.9 25.0 + - - +
133g VAL* 4.3 8.4 - - + -
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Residues in contact with ALA 95 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64e THR* 3.3 18.3 + - + +
67e GLY* 3.5 15.9 - - - -
68e ILE 3.7 20.2 - - - +
69e THR* 3.4 14.9 - - + +
90g ILE* 3.5 24.2 - - + -
93g GLY 3.1 0.8 + - - -
94g PRO* 1.3 80.0 - - - +
96g LEU* 1.3 62.4 + - - +
98g ASN* 3.3 1.9 + - - +
99g MET* 3.0 19.6 + - - +
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Residues in contact with LEU 96 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83g VAL* 4.3 6.1 - - + +
86g ALA* 3.9 28.5 - - + +
87g LEU* 3.8 37.2 - - + +
90g ILE* 4.2 5.1 - - + +
91g GLY 3.6 11.9 - - - +
92g SER* 3.9 11.2 - - - -
93g GLY 2.7 17.0 + - - +
95g ALA* 1.3 71.5 - - - +
97g VAL* 1.3 62.0 + - + +
99g MET* 3.1 5.2 + - + +
100g ILE* 2.8 52.2 + - + +
126g THR* 4.6 12.8 - - + -
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Residues in contact with VAL 97 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93g GLY* 3.8 7.6 - - - +
94g PRO* 3.0 10.1 + - + +
96g LEU* 1.3 79.7 - - + +
98g ASN* 1.3 66.4 + - - +
100g ILE* 3.3 0.6 + - + -
101g ASN* 3.1 33.4 + - - +
130g THR* 3.4 25.0 + - - +
131g GLY* 3.6 28.9 - - - +
132g TYR 4.8 2.9 - - - +
133g VAL* 3.7 31.0 - - + -
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Residues in contact with ASN 98 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67e GLY* 3.1 34.8 + - - -
69e THR* 4.4 8.1 - - + -
94g PRO* 2.9 11.5 + - - +
95g ALA* 3.5 7.4 - - - +
97g VAL* 1.3 82.3 - - - +
99g MET* 1.3 63.8 + - - +
101g ASN* 3.5 8.6 + - - +
102g GLY 3.3 15.1 + - - -
109h SER 3.5 22.8 - - - +
110h ALA* 3.7 3.1 - - - +
112h ASN* 5.2 8.7 - - - +
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Residues in contact with MET 99 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1968 T 4.1 11.9 - - - +
69e THR* 4.6 5.4 - - + -
70e GLY 5.3 0.2 - - - +
82g LYS* 4.7 12.6 - - - +
83g VAL* 6.3 0.4 - - - -
86g ALA* 3.8 24.0 - - + -
90g ILE* 3.7 23.1 - - + -
95g ALA 3.0 13.9 + - - +
96g LEU* 3.3 12.8 - - + +
98g ASN* 1.3 77.1 - - - +
100g ILE* 1.3 60.6 + - + +
102g GLY* 3.2 3.1 + - - -
103g LEU* 2.8 32.4 + - + +
106h TYR* 4.7 9.6 - - - -
110h ALA* 4.2 20.0 + - - +
111h PHE* 3.8 28.9 - - + -
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Residues in contact with ILE 100 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79g PHE* 5.0 3.4 - - + -
83g VAL* 4.3 19.3 - - + -
96g LEU* 2.8 46.8 + - + +
97g VAL* 3.9 3.8 - - + +
99g MET* 1.3 74.4 - - + +
101g ASN* 1.3 57.7 + - - +
103g LEU* 3.5 6.9 - - + +
104g LYS* 2.8 44.0 + - + +
122g VAL* 4.2 15.7 - - + -
126g THR* 4.1 22.9 - - + -
130g THR* 3.5 33.7 - - + +
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Residues in contact with ASN 101 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97g VAL* 3.1 35.0 + - - +
98g ASN* 3.7 9.2 + - - +
100g ILE* 1.3 77.2 - - - +
102g GLY* 1.3 61.5 + - - +
104g LYS* 3.5 8.0 + - - +
105g GLY* 3.2 17.5 + - - -
130g THR* 3.3 20.5 - - - +
131g GLY* 4.3 6.9 + - - -
109h SER* 4.2 8.9 + - - +
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Residues in contact with GLY 102 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98g ASN 3.3 4.4 + - - -
99g MET 3.2 5.8 + - - -
101g ASN* 1.3 76.8 - - - +
103g LEU* 1.3 60.6 + - - +
105g GLY* 3.1 3.7 + - - -
106g TYR 2.9 23.9 + - - -
105h GLY 5.3 0.2 - - - -
106h TYR* 3.5 19.2 - - - -
109h SER* 3.0 24.3 + - - -
110h ALA* 4.0 10.1 - - - -
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Residues in contact with LEU 103 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79g PHE* 3.6 16.2 - - + -
82g LYS* 3.5 47.3 - - + +
83g VAL* 3.6 31.4 - - + +
99g MET* 2.8 23.3 + - + +
100g ILE* 3.2 8.9 + - + +
102g GLY* 1.3 73.2 - - - +
104g LYS* 1.3 64.3 + - - +
106g TYR* 3.1 11.2 + - + +
107g TYR* 3.0 41.4 + - + -
106h TYR* 3.9 10.8 - - + -
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Residues in contact with LYS 104 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79g PHE* 3.8 28.3 - - + -
100g ILE* 2.8 34.5 + - + +
101g ASN* 3.7 7.7 + - - +
103g LEU* 1.3 72.2 - - - +
105g GLY* 1.3 58.1 + - - +
107g TYR* 3.2 1.4 + - - +
108g ILE* 2.8 54.7 + - + +
115g PRO* 5.0 4.9 - - - +
118g LEU* 4.8 6.1 - - + -
119g ASP* 2.7 36.4 + - - +
122g VAL* 5.0 2.0 - - + -
129g PRO* 6.1 0.4 - - - +
130g THR* 4.6 12.4 - - + +
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Residues in contact with GLY 105 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101g ASN 3.2 8.1 + - - -
102g GLY* 3.1 8.2 + - - -
104g LYS* 1.3 77.9 - - - +
106g TYR* 1.3 58.0 + - - +
108g ILE* 4.5 6.0 - - - +
109g SER* 2.6 36.3 + - - -
102h GLY* 4.4 3.6 - - - -
105h GLY* 5.9 2.7 - - - -
106h TYR 5.3 2.5 - - - -
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Residues in contact with TYR 106 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437 A 3.8 4.9 + - - -
1447 T 2.9 19.3 + - - -
82g LYS* 5.6 3.4 - - - -
102g GLY 2.9 12.1 + - - +
103g LEU* 3.1 15.2 + - + +
105g GLY* 1.3 75.0 - - - +
107g TYR* 1.3 85.1 + + - +
110g ALA* 2.8 41.5 + - + +
111g PHE* 3.7 26.3 - + - -
82h LYS* 2.8 39.8 + - - -
99h MET* 4.6 7.7 - - - +
102h GLY 3.7 15.6 + - - -
103h LEU* 4.0 13.0 - - + -
106h TYR* 3.7 31.4 - + + +
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Residues in contact with TYR 107 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437 A 4.5 5.0 - - + +
1447 T 3.3 35.2 + - - -
75g ILE* 3.5 37.9 - - + -
78g GLY* 3.5 9.4 - - - -
79g PHE* 3.7 31.2 - + + -
82g LYS* 5.2 1.3 - - + -
103g LEU* 3.0 26.2 + - + +
104g LYS 4.0 1.6 - - - +
106g TYR* 1.3 98.7 - + - +
108g ILE* 1.3 66.4 + - - +
111g PHE* 3.1 40.8 + + + -
113g ALA* 3.0 26.2 + - + +
118g LEU* 4.4 7.9 - - + -
71j PRO* 6.5 1.1 - - + -
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Residues in contact with ILE 108 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104g LYS* 2.8 45.9 + - + +
105g GLY* 4.1 5.8 - - - +
107g TYR* 1.3 72.7 - - - +
109g SER* 1.3 62.5 + - - +
112g ASN* 3.1 25.1 - - - +
113g ALA 3.6 16.6 - - - +
115g PRO* 3.9 31.4 - - + -
118g LEU* 3.3 21.1 - - + -
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Residues in contact with SER 109 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105g GLY* 2.6 22.2 + - - -
108g ILE* 1.3 84.2 - - - +
110g ALA* 1.3 61.6 + - - +
112g ASN* 4.0 10.4 - - - +
98h ASN* 3.5 17.5 - - - +
101h ASN* 4.2 5.8 + - - +
102h GLY* 2.9 22.2 + - - -
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Residues in contact with ALA 110 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106g TYR* 2.8 25.4 + - + +
109g SER* 1.3 80.8 + - - +
111g PHE* 1.3 62.6 + - + +
112g ASN* 5.1 1.5 + - - -
98h ASN* 3.6 13.5 - - - +
99h MET* 3.9 35.1 + - - +
102h GLY* 4.1 4.7 - - - -
69j THR* 2.6 34.3 + - - +
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Residues in contact with PHE 111 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437 A 3.8 24.5 - - - -
75g ILE* 4.8 13.3 - - + +
106g TYR* 3.7 34.3 - + - -
107g TYR* 3.1 47.1 + + + +
110g ALA* 1.3 79.6 - - + +
112g ASN* 1.3 74.7 + - - +
113g ALA* 3.3 1.9 + - - +
99h MET* 3.7 27.6 - - + -
69j THR* 3.4 17.0 - - - +
70j GLY* 3.5 31.9 - - - -
71j PRO* 4.6 3.6 - - + -
72j ASN* 3.3 19.8 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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