Contacts of the helix formed by residues 93 - 109 (chain h) in PDB entry 3J7Y
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 ASP 93 (chain h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91h LEU 2.5 16.3 + - - +
92h GLU* 1.3 81.3 - - - +
94h SER* 1.3 65.0 + - - +
95h ARG* 4.8 2.0 - - + +
96h LEU* 3.8 15.3 + - + +
97h LYS* 3.4 19.9 + - - +
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Residues in contact with SER 94 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LEU* 3.7 21.3 - - - +
63F GLN* 4.5 5.5 + - - -
79F LEU* 3.2 28.9 + - - +
81F ASP* 4.9 10.6 + - - -
92h GLU 3.5 4.7 + - - -
93h ASP* 1.3 71.3 - - - +
95h ARG* 1.3 61.3 + - - +
97h LYS* 3.2 8.6 + - - +
98h PHE* 2.9 28.4 + - - +
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Residues in contact with ARG 95 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F GLU* 4.0 17.2 + - - -
46F PRO* 3.3 49.1 + - + +
48F LEU* 3.3 24.4 - - + +
93h ASP* 4.8 2.0 - - + +
94h SER* 1.3 78.9 - - - +
96h LEU* 1.3 58.5 + - - +
98h PHE* 3.2 9.1 + - - +
99h ASN* 2.9 37.7 + - - +
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Residues in contact with LEU 96 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74h VAL* 6.5 1.8 - - + -
77h VAL* 3.4 27.4 - - + -
78h PHE* 3.7 32.1 - - + +
89h ILE* 5.9 4.3 - - + -
90h SER 5.0 0.9 - - - +
91h LEU* 3.6 44.6 - - + +
93h ASP* 3.8 16.6 + - + +
95h ARG* 1.3 79.5 - - - +
97h LYS* 1.3 61.3 + - - +
99h ASN* 3.2 9.4 + - - +
100h LEU* 2.9 33.9 + - + +
123h VAL* 6.2 0.9 - - + -
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Residues in contact with LYS 97 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F GLN* 3.3 39.2 - - - +
79F LEU* 4.5 7.6 - - + -
91h LEU* 3.5 38.0 - - + +
92h GLU* 5.0 4.7 - - - +
93h ASP 3.4 11.0 + - - +
94h SER* 3.2 11.1 + - - +
96h LEU* 1.3 81.2 - - - +
98h PHE* 1.3 62.6 + - - +
100h LEU* 4.7 0.9 - - - -
101h LEU* 3.0 45.3 + - + +
117h LEU* 3.9 23.2 + - + +
120h MET* 2.8 29.9 + - - +
121h CYS* 5.2 1.6 - - - +
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Residues in contact with PHE 98 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F GLU 5.3 0.7 - - - -
46F PRO* 3.4 42.0 - - + -
48F LEU* 4.5 6.1 - - + -
65F TRP* 3.8 16.8 - + - -
76F ARG 3.1 29.6 - - - -
77F VAL* 5.0 0.4 - - - -
78F GLY 3.8 20.6 - - - -
79F LEU* 4.3 19.9 - - + +
94h SER 2.9 13.1 + - - +
95h ARG* 3.2 7.2 + - - +
97h LYS* 1.3 77.2 - - - +
99h ASN* 1.3 70.3 + - - +
102h ALA* 3.0 49.8 + - + +
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Residues in contact with ASN 99 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F PRO* 4.5 8.6 - - - +
77h VAL* 4.1 19.2 - - + +
78h PHE* 5.8 1.9 - - - -
95h ARG* 2.9 23.2 + - - +
96h LEU* 3.4 10.7 - - - +
98h PHE* 1.3 93.9 - - - +
100h LEU* 1.3 57.1 + - - +
102h ALA* 4.2 0.6 - - - +
103h HIS* 2.7 51.6 + - + -
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Residues in contact with LEU 100 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70h LEU* 4.2 15.3 - - + -
73h TYR* 4.3 16.4 - - + -
74h VAL* 4.2 19.1 - - + +
77h VAL* 4.6 9.6 - - + -
91h LEU* 4.7 13.5 - - + -
96h LEU* 2.9 26.9 + - + +
97h LYS* 3.2 3.8 + - - +
99h ASN* 1.3 75.7 - - - +
101h LEU* 1.3 78.6 + - + +
103h HIS* 3.2 4.1 + - - +
104h LEU* 2.9 65.0 + - + +
123h VAL* 5.5 4.9 - - + -
126h VAL* 4.4 8.1 - - + -
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Residues in contact with LEU 101 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F TRP* 3.8 23.6 - - + -
79F LEU* 5.3 0.2 - - + -
91h LEU* 4.5 1.6 - - + -
97h LYS* 3.0 47.7 + - + +
100h LEU* 1.3 92.4 - - + +
102h ALA* 1.3 58.2 + - - +
104h LEU* 3.2 7.7 + - + +
105h ALA* 2.9 28.8 + - - +
112h VAL* 4.0 21.2 - - + +
117h LEU* 4.1 17.3 - - + -
120h MET* 5.1 2.2 - - + -
126h VAL* 3.7 36.6 - - + -
130h TYR* 3.8 3.4 + - + -
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Residues in contact with ALA 102 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F TRP* 4.0 9.1 - - + -
76F ARG* 3.0 27.8 + - + +
98h PHE* 3.0 45.0 + - + +
99h ASN 4.2 1.8 - - - +
101h LEU* 1.3 78.1 - - - +
103h HIS* 1.3 61.7 + - + +
105h ALA* 3.2 3.3 + - - -
106h ASP* 2.9 26.8 + - - +
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Residues in contact with HIS 103 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73h TYR* 3.4 36.5 + + + +
77h VAL* 4.6 11.2 - - + -
99h ASN* 2.7 42.4 + - + +
100h LEU 3.2 5.4 + - - +
102h ALA* 1.3 83.1 - - + +
104h LEU* 1.3 56.7 - - - +
106h ASP* 3.2 11.1 + - - +
107h ASP* 2.9 34.1 + - - +
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Residues in contact with LEU 104 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66h LEU* 5.7 2.0 - - + -
69h ARG* 5.8 2.2 - - + -
70h LEU* 4.0 26.9 - - + -
73h TYR* 4.1 21.3 - - + -
100h LEU* 2.9 49.1 + - + +
101h LEU* 3.4 5.6 - - - +
103h HIS* 1.3 77.1 - - - +
105h ALA* 1.3 51.1 + - - +
107h ASP* 3.2 4.8 + - + -
108h LEU* 2.7 54.7 + - + +
126h VAL* 4.0 7.0 - - + -
130h TYR* 3.1 37.2 - - + +
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Residues in contact with ALA 105 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F TRP* 5.9 1.6 - - + -
76F ARG* 3.4 21.8 - - + +
101h LEU 2.9 13.0 + - - +
102h ALA* 3.4 10.1 - - - +
104h LEU* 1.3 75.3 - - - +
106h ASP* 1.3 58.2 - - - +
109h GLY* 2.7 33.6 + - - -
110h HIS 3.5 22.8 + - - +
111h VAL* 4.0 16.9 - - + +
112h VAL 5.2 0.9 - - - +
130h TYR* 3.5 0.8 + - - +
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Residues in contact with ASP 106 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F ARG* 3.2 11.7 + - - +
102h ALA 2.9 12.4 + - - +
103h HIS* 3.2 16.4 + - - +
105h ALA* 1.3 78.3 - - - +
107h ASP* 1.3 66.4 + - - +
109h GLY* 4.2 2.8 + - - -
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Residues in contact with ASP 107 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69h ARG* 2.6 40.0 + - + +
73h TYR* 2.6 36.0 + - + -
103h HIS 2.9 9.7 + - - +
104h LEU* 3.6 7.4 - - + +
106h ASP* 1.3 86.4 - - - +
108h LEU* 1.3 67.5 + - + +
109h GLY 3.6 0.3 + - - -
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Residues in contact with LEU 108 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60h TYR* 4.1 25.0 - - + +
63h PRO* 4.0 30.7 - - + -
66h LEU* 4.4 12.3 - - + -
69h ARG* 6.4 2.2 - - + -
104h LEU* 2.7 33.8 + - + +
107h ASP* 1.3 78.4 - - + +
109h GLY* 1.3 61.7 + - - +
110h HIS* 4.3 6.3 - - + -
130h TYR* 3.4 38.1 - - + -
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Residues in contact with GLY 109 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56h ARG* 4.8 16.6 + - - -
57h SER 5.4 2.9 - - - +
59h ALA 5.5 1.9 - - - +
60h TYR* 5.0 3.1 - - - +
105h ALA 2.7 21.5 + - - -
106h ASP 4.2 2.6 + - - -
107h ASP 3.4 3.0 + - - -
108h LEU* 1.3 73.5 - - - +
110h HIS* 1.3 60.2 + - - +
111h VAL* 4.2 1.8 - - - -
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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
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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