Contacts of the helix formed by residues 96 - 109 (chain i) 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 i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367P LEU* 3.8 18.9 - - - +
370P LEU* 4.6 3.0 - - - +
403P HIS* 4.9 12.8 - - - -
95i CYS* 1.3 73.9 - - - +
97i SER* 1.4 55.2 + - - +
99i ILE* 3.5 4.4 + - - +
100i ALA* 3.0 28.5 + - - +
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Residues in contact with SER 97 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403P HIS* 4.6 14.8 + - - -
95d CYS* 5.7 3.5 - - - -
97d SER* 5.7 5.2 + - - -
95i CYS* 3.3 7.5 - - - +
96i GLY* 1.4 73.7 - - - +
98i ALA* 1.4 58.8 + - - +
100i ALA* 3.3 8.9 + - - +
101i SER* 3.0 31.2 + - - -
129i LEU* 4.5 2.8 - - - +
131i LEU* 5.1 13.3 - - - +
135i LYS* 6.0 4.7 - - - -
138i CYS* 4.9 8.3 - - - -
139i SER* 5.0 5.4 - - - -
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Residues in contact with ALA 98 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73i MET* 4.1 12.1 - - + -
94i GLY* 4.8 0.2 - - - -
95i CYS* 3.3 14.5 + - - +
97i SER* 1.4 74.1 - - - +
99i ILE* 1.3 60.7 + - - +
101i SER* 3.3 2.7 + - - -
102i SER* 3.1 30.8 + - - -
138i CYS* 3.2 43.6 - - + +
139i SER* 4.4 10.8 - - - +
142i ALA* 3.5 7.1 - - + +
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Residues in contact with ILE 99 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367P LEU* 3.4 37.7 - - + +
370P LEU* 4.0 16.6 - - + -
371P LYS* 3.9 14.5 - - + +
73i MET* 3.9 12.3 - - + -
92i THR* 3.5 37.2 - - - +
93i PHE 3.7 6.7 - - - +
94i GLY* 3.7 19.5 - - - -
95i CYS 3.1 20.6 + - - +
96i GLY 3.8 2.5 - - - +
98i ALA* 1.3 74.2 - - - +
100i ALA* 1.3 58.8 + - - +
102i SER* 3.3 7.3 + - - -
103i SER* 3.0 27.2 + - - -
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Residues in contact with ALA 100 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370P LEU* 3.8 8.5 - - + -
375P LEU* 3.5 31.8 - - + +
377P SER* 5.5 0.4 - - - +
403P HIS* 5.9 4.5 - - + -
96i GLY 3.0 14.7 + - - +
97i SER* 3.4 13.0 - - - +
99i ILE* 1.3 73.9 - - - +
101i SER* 1.3 63.0 + - - +
103i SER* 2.8 22.0 + - - -
104i LEU* 3.3 8.5 + - - +
129i LEU* 4.1 10.4 - - + +
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Residues in contact with SER 101 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97i SER 3.0 15.1 + - - -
98i ALA* 3.3 10.1 + - - -
100i ALA* 1.3 74.8 - - - +
102i SER* 1.4 57.0 + - - +
104i LEU* 3.6 2.1 + - - +
105i ALA* 3.0 29.6 + - - +
125i ILE* 4.0 34.7 + - - +
126i ALA* 5.5 1.0 + - - -
129i LEU* 3.3 22.6 - - - +
139i SER* 4.3 12.5 + - - -
142i ALA* 4.2 4.7 - - - -
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Residues in contact with SER 102 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371P LYS* 3.5 27.2 + - - -
73i MET* 3.7 16.1 - - - -
75i LEU* 4.6 9.9 - - - +
98i ALA 3.1 14.8 + - - -
99i ILE 3.5 7.6 - - - -
100i ALA 3.3 0.2 - - - -
101i SER* 1.4 75.6 - - - +
103i SER* 1.4 62.3 + - - +
105i ALA* 3.5 7.6 + - - +
106i THR* 2.9 27.9 + - - -
142i ALA* 3.2 20.1 + - - +
146i ILE* 5.5 0.4 - - - -
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Residues in contact with SER 103 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370P LEU 3.5 17.7 + - - -
371P LYS* 3.1 27.8 - - - -
373P VAL 3.4 9.6 - - - +
374P ALA* 4.8 0.2 - - - -
375P LEU* 3.4 14.9 - - - +
99i ILE 3.0 11.4 + - - -
100i ALA* 2.8 23.9 + - - -
102i SER* 1.4 76.5 - - - +
104i LEU* 1.4 61.7 + - - +
106i THR* 3.4 13.4 + - - -
107i GLU* 3.4 21.5 + - - +
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Residues in contact with LEU 104 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4564 GLN* 5.2 0.7 - - - +
4574 HIS* 3.5 17.0 - - + -
67P THR* 6.5 0.9 - - - -
68P PRO* 6.6 0.2 - - + -
374P ALA* 4.0 17.7 - - + -
375P LEU* 3.7 11.7 - - + -
407P ARG* 3.9 21.3 - - - +
100i ALA 3.3 13.3 + - - +
101i SER* 4.1 3.1 - - - +
103i SER* 1.4 76.9 + - - +
105i ALA* 1.4 59.2 + - - +
107i GLU* 3.3 8.7 + - + +
108i TRP* 3.0 27.4 + - - +
125i ILE 5.3 1.6 - - - +
128i GLU* 3.1 51.8 - - + +
129i LEU* 3.6 13.0 - - + +
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Residues in contact with ALA 105 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101i SER 3.0 19.2 + - - +
102i SER* 3.5 7.9 - - - +
103i SER 3.3 0.2 - - - -
104i LEU* 1.4 75.5 - - - +
106i THR* 1.4 59.8 + - - +
108i TRP* 3.2 12.2 + - - +
109i VAL* 3.1 27.5 + - - +
120i ILE* 4.1 3.1 - - + +
125i ILE* 3.6 29.7 - - + +
146i ILE* 3.7 19.3 - - + -
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Residues in contact with THR 106 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371P LYS 5.7 0.2 - - - -
372P ASP 6.1 0.4 - - - +
425P LYS* 6.3 0.4 - - + -
75i LEU* 4.4 9.5 - - - +
77i ILE* 5.0 8.1 - - + -
85i ILE* 5.8 2.0 - - + +
87i ASP* 5.4 4.5 - - - +
88i ALA* 3.6 29.6 - - + +
90i PHE* 3.6 20.2 - - + -
102i SER 2.9 14.3 + - - -
103i SER* 3.5 9.8 + - - -
104i LEU 3.3 0.4 - - - -
105i ALA* 1.4 75.9 - - - +
107i GLU* 1.4 63.4 + - - +
109i VAL* 3.3 12.5 - - + +
110i LYS* 3.1 29.2 + - + +
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Residues in contact with GLU 107 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P PRO* 3.9 33.5 - - + +
372P ASP 4.5 4.1 - - - +
373P VAL* 3.0 27.4 - - - +
374P ALA* 3.5 22.2 - - + +
409P GLY* 4.1 17.4 - - - +
87i ASP* 5.8 0.2 - - - +
103i SER 3.4 9.9 + - - +
104i LEU* 3.3 12.9 + - + +
106i THR* 1.4 83.7 - - - +
108i TRP* 1.3 54.2 + - - +
109i VAL 3.1 0.2 - - - -
110i LYS* 3.1 52.6 + - + +
112i LYS* 3.8 5.1 + - - -
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Residues in contact with TRP 108 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I GLU* 4.6 13.3 + - - -
197I LYS* 3.5 17.3 - - - -
199I ASP* 4.7 4.3 - - - -
201I SER* 5.6 2.0 - - - -
208I LYS* 5.3 7.4 - - + -
67P THR 3.2 27.6 - - - -
69P LEU* 4.2 8.7 - - + -
104i LEU 3.0 14.0 + - - +
105i ALA* 3.3 13.2 - - - +
107i GLU* 1.3 72.7 - - - +
109i VAL* 1.4 60.7 + - + +
112i LYS* 3.0 39.9 + - + +
116i GLU* 5.0 10.3 + - + +
120i ILE* 4.0 26.2 - - + +
124i ASP* 3.9 29.5 + - - +
127i LYS* 4.3 15.5 - - + -
128i GLU* 3.3 41.3 - - + +
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Residues in contact with VAL 109 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77i ILE* 5.5 6.1 - - + -
85i ILE* 3.5 35.3 - - + +
105i ALA 3.1 12.3 + - - +
106i THR* 3.3 20.0 - - + +
108i TRP* 1.4 81.0 - - + +
110i LYS* 1.4 61.0 + - - +
112i LYS* 3.6 22.2 + - - +
113i THR 5.6 0.2 - - - +
116i GLU* 4.8 2.2 - - + +
117i ALA* 3.7 36.1 - - + +
120i ILE* 4.0 18.6 - - + -
146i ILE* 5.7 6.7 - - + -
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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