Contacts of the helix formed by residues 101 - 112 (chain K) 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 VAL 101 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62K THR* 3.9 16.2 - - - +
99K ASP* 3.3 14.1 - - - +
100K PRO* 1.3 80.3 - - + +
102K ALA* 1.3 64.8 + - - +
103K ILE 3.3 1.3 + - - -
104K VAL* 3.6 5.0 + - - +
105K LYS* 3.3 34.9 + - + +
127K LEU* 3.5 49.2 - - + +
129K PRO* 4.2 16.4 - - + -
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Residues in contact with ALA 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K LEU* 3.4 27.8 - - + -
99K ASP* 3.0 31.7 + - + +
101K VAL* 1.3 77.6 - - - +
103K ILE* 1.3 58.1 + - - +
105K LYS* 3.2 9.2 + - - +
106K LEU* 2.9 37.9 + - + +
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Residues in contact with ILE 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2239A A 5.6 0.4 - - - +
28K PRO* 3.9 13.5 - - + -
65K ILE* 4.3 9.9 - - + -
67K PHE* 3.7 23.8 - - + -
72K TRP* 3.5 25.4 - - + -
77K TYR* 3.5 31.3 + - + +
92K ALA* 3.3 31.0 - - + +
95K LEU* 4.5 11.0 - - + -
96K HIS* 3.9 12.8 - - + +
99K ASP 4.5 0.2 + - - -
100K PRO 4.1 4.0 + - - +
101K VAL 3.4 0.8 - - - -
102K ALA* 1.3 79.1 - - - +
104K VAL* 1.3 65.1 + - - +
106K LEU* 3.4 6.5 + - - +
107K ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K PRO* 4.4 12.3 - - + -
31K LEU* 4.7 15.5 - - + -
32K ALA* 5.4 1.8 - - + -
59K ILE* 4.1 10.1 - - + -
62K THR* 3.7 21.1 - - + -
65K ILE* 3.2 32.5 - - + +
101K VAL 3.6 5.8 + - - +
102K ALA 3.3 0.2 - - - -
103K ILE* 1.3 78.1 - - - +
105K LYS* 1.3 58.2 + - - +
107K ALA* 3.2 4.7 + - - +
108K ILE* 2.9 50.0 + - + +
127K LEU* 3.9 14.6 - - + -
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Residues in contact with LYS 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K VAL* 3.3 23.5 + - + +
102K ALA* 3.3 12.8 - - - +
104K VAL* 1.3 80.0 - - - +
106K LEU* 1.3 58.2 + - + +
108K ILE* 3.2 7.6 + - - +
109K TYR* 2.9 29.2 + - - +
122K MET* 3.5 30.4 - - + +
125K LEU* 4.9 4.3 - - - -
127K LEU* 3.4 27.2 - - + +
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Residues in contact with LEU 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2238A A 4.3 4.4 + - - +
2239A A 5.3 1.3 - - - +
77K TYR* 3.3 39.5 - - + -
95K LEU* 3.9 16.6 - - + -
102K ALA* 2.9 21.3 + - + +
103K ILE 3.7 4.5 - - - +
104K VAL 3.3 0.2 - - - -
105K LYS* 1.3 77.3 - - + +
107K ALA* 1.3 58.1 + - - +
109K TYR* 3.2 14.4 + - + +
110K GLY* 2.9 25.6 + - - -
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Residues in contact with ALA 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2238A A 2.5 34.0 + - - +
2239A A 3.4 18.1 + - - +
28K PRO* 4.7 2.9 - - + -
29K GLY* 4.0 16.4 - - - +
32K ALA* 3.8 15.9 - - + -
103K ILE 3.1 11.2 + - - +
104K VAL* 3.4 10.5 - - - +
106K LEU* 1.3 76.5 - - - +
108K ILE* 1.3 61.3 + - - +
110K GLY 3.2 0.2 + - - -
111K MET* 3.0 11.5 + - + +
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Residues in contact with ILE 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K ALA* 3.4 24.7 - - + -
35K ALA* 3.8 8.3 - - + -
36K SER* 4.6 6.3 - - - -
39K LEU* 3.5 29.8 - - + -
59K ILE* 3.6 21.5 - - + -
104K VAL* 2.9 35.8 + - + +
105K LYS 3.5 7.6 - - - +
107K ALA* 1.3 76.6 - - - +
109K TYR* 1.3 62.7 + - - +
111K MET* 3.2 6.7 + - - +
112K LEU* 3.0 24.0 + - + +
122K MET* 4.0 11.4 - - - -
125K LEU* 3.7 18.8 - - + -
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Residues in contact with TYR 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2703A C 3.6 16.2 - - - -
2704A A 3.4 24.7 + - - -
2705A U 6.1 1.4 - - - -
105K LYS 2.9 12.6 + - - +
106K LEU* 3.3 19.1 - - + +
108K ILE* 1.3 77.7 - - - +
110K GLY* 1.3 61.6 + - - +
112K LEU* 3.1 11.9 + - - +
118K ARG* 3.3 79.9 + - + +
119K ARG* 4.3 23.5 + - + +
122K MET* 3.7 32.5 - - + -
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Residues in contact with GLY 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2237A A 3.9 10.6 - - - -
2238A A 3.1 29.6 - - - -
2703A C 4.9 4.5 - - - -
106K LEU 2.9 13.2 + - - -
107K ALA 3.2 0.4 + - - -
109K TYR* 1.3 79.0 - - - +
111K MET* 1.3 61.1 - - - +
112K LEU 3.5 0.3 - - - +
114K LYS* 2.7 29.7 + - - -
118K ARG* 4.8 0.4 - - - -
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Residues in contact with MET 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2237A A 5.3 5.1 - - - +
2238A A 2.9 30.4 + - + +
2239A A 2.9 41.1 - - + +
29K GLY* 3.3 21.5 - - - +
32K ALA* 3.9 11.7 - - + +
33K ALA* 3.7 22.9 - - + -
36K SER* 3.3 23.9 + - - +
40K GLN* 4.7 5.4 + - - -
107K ALA 3.0 13.0 + - - +
108K ILE 3.2 2.7 + - - +
110K GLY* 1.3 78.0 - - - +
112K LEU* 1.3 61.4 + - - +
113K PRO* 3.8 1.6 - - - +
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Residues in contact with LEU 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K SER* 3.5 32.3 - - - +
39K LEU* 3.8 16.8 - - + -
40K GLN* 3.9 17.3 - - + +
108K ILE 3.0 15.7 + - - +
109K TYR 3.1 12.6 + - - +
110K GLY 3.5 8.1 - - - +
111K MET* 1.3 79.8 - - - +
113K PRO* 1.3 71.8 - - + +
114K LYS* 3.6 9.9 + - - +
118K ARG* 3.8 17.6 - - + +
121K MET* 4.0 24.2 - - + -
122K MET* 3.7 30.3 - - - -
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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