Contacts of the helix formed by residues 96 - 109 (chain k) in PDB entry 5KZ5
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 96 (chain k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95k CYS* 1.3 72.9 - - - +
97k SER* 1.4 55.6 + - - +
99k ILE* 3.4 19.2 + - - +
100k ALA* 3.2 25.6 + - - +
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Residues in contact with SER 97 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95k CYS* 3.8 9.7 - - - +
96k GLY* 1.4 73.2 - - - +
98k ALA* 1.4 58.4 + - - +
100k ALA* 4.0 8.1 - - - +
101k SER* 3.1 28.6 + - - -
129k LEU* 4.1 4.2 - - - +
131k LEU* 4.5 17.7 - - - +
135k LYS* 3.5 24.8 + - - -
138k CYS* 3.7 15.7 - - - -
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Residues in contact with ALA 98 (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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69k CYS* 5.3 3.1 - - + -
92k THR* 5.1 1.8 - - - +
93k PHE 4.2 10.8 - - - +
94k GLY* 4.1 4.7 - - - -
95k CYS* 3.0 25.9 + - - +
97k SER* 1.4 78.0 + - - +
99k ILE* 1.4 58.5 + - - +
101k SER* 3.4 3.1 + - - -
102k SER* 2.9 36.9 + - - +
138k CYS* 3.7 30.4 - - + +
141k LEU* 6.2 1.3 - - + -
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Residues in contact with ILE 99 (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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364Q GLU* 4.0 23.8 - - + +
367Q LEU* 3.8 29.4 - - + -
368Q MET* 3.5 45.8 - - + +
375Q LEU* 5.8 0.2 - - - -
404Q SER* 6.4 1.1 - - - -
90k PHE* 3.8 5.6 - - + -
92k THR* 4.1 14.3 - - + +
93k PHE 5.9 0.2 - - - -
94k GLY 4.3 2.7 - - - +
95k CYS 3.3 12.3 - - - +
96k GLY* 3.4 18.1 + - - +
98k ALA* 1.4 74.1 - - - +
100k ALA* 1.3 56.8 + - - +
102k SER 3.6 0.2 + - - -
103k SER* 2.9 34.1 + - - -
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Residues in contact with ALA 100 (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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367Q LEU* 6.4 0.2 - - - -
375Q LEU* 4.0 26.2 - - + -
96k GLY 3.2 12.8 + - - +
97k SER* 4.1 4.9 - - - +
99k ILE* 1.3 77.7 - - - +
101k SER* 1.4 62.6 + - - +
103k SER* 3.5 2.2 + - - -
104k LEU* 3.2 30.5 + - - +
129k LEU* 3.8 25.6 - - + -
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Residues in contact with SER 101 (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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97k SER 3.1 21.2 + - - -
98k ALA* 3.4 4.7 + - - -
100k ALA* 1.4 75.8 - - - +
102k SER* 1.3 57.3 + - - +
104k LEU* 3.7 4.1 + - - +
105k ALA* 3.0 27.8 + - - +
125k ILE* 3.4 24.7 - - - +
129k LEU* 3.6 15.5 - - - +
131k LEU* 4.3 4.6 - - - +
138k CYS 5.2 0.2 - - - -
139k SER* 3.3 30.5 + - - -
142k ALA* 4.6 1.1 - - - -
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Residues in contact with SER 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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73k MET* 3.6 19.7 - - - +
90k PHE* 3.6 24.0 - - - -
92k THR* 3.5 15.7 + - - -
98k ALA* 2.9 22.7 + - - +
99k ILE 3.8 0.7 - - - -
101k SER* 1.3 75.4 - - - +
103k SER* 1.3 56.2 + - - +
105k ALA* 3.2 4.2 + - - +
106k THR* 3.0 30.5 + - - -
138k CYS 4.9 3.1 + - - -
141k LEU* 5.7 0.3 - - - +
142k ALA* 3.7 16.0 + - - +
146k ILE* 5.2 0.2 - - - +
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Residues in contact with SER 103 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367Q LEU* 3.9 5.9 - - - +
372Q ASP* 5.5 3.0 + - - +
373Q VAL* 3.4 47.6 + - - +
375Q LEU* 5.8 0.9 - - - -
90k PHE* 3.3 26.1 - - - -
99k ILE 2.9 21.6 + - - -
100k ALA* 3.9 5.6 - - - -
101k SER 3.4 0.2 - - - -
102k SER* 1.3 70.8 - - - +
104k LEU* 1.4 66.8 + - - +
106k THR* 3.3 6.4 + - - -
107k GLU* 3.1 17.8 + - - +
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Residues in contact with LEU 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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67Q THR 3.9 18.6 + - - +
373Q VAL 3.8 6.7 - - - +
374Q ALA* 3.7 39.0 - - - +
375Q LEU* 3.8 15.7 - - + +
100k ALA 3.2 20.3 + - - +
101k SER* 3.7 7.0 - - - +
103k SER* 1.4 78.5 - - - +
105k ALA* 1.3 55.2 + - - +
107k GLU* 3.3 4.8 + - + +
108k TRP* 3.0 30.4 + - - +
125k ILE* 4.7 8.1 - - + +
128k GLU* 3.7 34.5 - - + +
129k LEU* 3.9 16.6 - - + -
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Residues in contact with ALA 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 SER 3.0 15.8 + - - +
102k SER 3.2 9.6 + - - +
104k LEU* 1.3 76.2 - - - +
106k THR* 1.4 61.0 + - - +
108k TRP* 3.3 11.6 + - - +
109k VAL* 3.4 8.8 + - - +
120k ILE* 3.6 6.1 - - + +
125k ILE* 3.5 26.6 - - + +
142k ALA* 3.9 15.9 - - + -
146k ILE* 3.4 25.3 - - + +
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Residues in contact with THR 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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371Q LYS* 3.7 36.6 - - + -
372Q ASP 5.8 0.4 - - - -
73k MET* 4.9 1.2 - - - +
75k LEU* 4.2 20.5 - - + +
77k ILE* 5.8 0.4 - - + -
85k ILE* 5.8 2.8 - - + +
88k ALA* 4.1 15.0 - - + -
90k PHE* 3.8 17.0 - - - -
102k SER 3.0 15.1 + - - -
103k SER* 3.3 6.5 + - - -
105k ALA* 1.4 73.5 - - - +
107k GLU* 1.4 60.9 + - - +
109k VAL* 3.2 12.5 - - + +
110k LYS* 3.2 21.2 + - - +
146k ILE* 3.8 8.3 - - - +
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Residues in contact with GLU 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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67Q THR* 4.3 3.8 - - - +
68Q PRO* 3.7 36.2 - - + +
371Q LYS* 5.4 1.3 - - - +
372Q ASP* 3.6 18.7 - - - +
373Q VAL 3.2 43.0 + - - +
374Q ALA* 3.9 11.0 + - + -
408Q PHE* 4.1 4.1 - - - +
409Q GLY 4.2 11.6 - - - +
410Q ILE* 5.6 0.3 - - - +
103k SER 3.1 6.3 + - - +
104k LEU* 3.3 11.4 + - + +
106k THR* 1.4 74.8 - - - +
108k TRP* 1.3 60.4 + - - +
110k LYS* 3.3 47.8 + - - +
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Residues in contact with TRP 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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184K GLU* 3.5 21.1 - - + -
67Q THR 3.4 25.1 - - - +
68Q PRO* 4.7 0.2 - - - -
69Q LEU* 3.5 36.9 + - + -
104k LEU 3.0 16.6 + - - +
105k ALA* 3.5 8.5 - - - +
106k THR 3.3 0.2 - - - -
107k GLU* 1.3 75.0 - - - +
109k VAL* 1.4 62.6 + - + +
110k LYS 4.4 0.9 - - - -
112k LYS* 3.1 38.6 - - - +
120k ILE* 3.8 32.9 - - + +
124k ASP* 3.6 35.4 - - + +
125k ILE* 4.9 3.1 - - + -
127k LYS* 3.9 15.9 - - - -
128k GLU* 3.5 40.6 - - + -
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Residues in contact with VAL 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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75k LEU* 5.9 1.8 - - + -
77k ILE* 6.4 0.9 - - + -
85k ILE* 3.4 31.1 - - + +
105k ALA 3.8 11.7 - - - +
106k THR* 3.2 21.3 - - + +
108k TRP* 1.4 83.2 - - + +
110k LYS* 1.3 59.9 + - - +
111k GLY 3.3 0.7 + - - -
112k LYS* 3.0 22.7 + - + +
117k ALA* 3.7 40.4 - - + +
120k ILE* 3.9 15.7 - - + -
146k ILE* 4.0 18.4 - - + -
150k LEU* 5.9 0.7 - - + -
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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