Contacts of the helix formed by residues 99 - 115 (chain H) 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 ALA 99 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G ARG* 3.5 5.1 - - - +
97H ARG 3.5 0.8 - - - -
98H LEU* 1.4 75.4 - - - +
100H GLU* 1.4 65.3 + - + +
102H THR* 3.5 4.0 + - - -
103H LEU* 3.4 28.2 + - + +
147H LYS* 6.2 2.5 - - + -
152H LYS* 3.8 36.1 - - + +
154H ILE* 3.8 9.5 - - + +
168H TRP* 3.6 28.0 - - + +
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Residues in contact with GLU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G ARG* 5.4 4.1 + - - +
97H ARG* 3.4 55.1 + - + +
98H LEU 3.5 0.2 - - - -
99H ALA* 1.4 75.6 - - + +
101H GLU* 1.4 64.0 + - - +
103H LEU* 3.3 21.6 + - - +
104H ASP* 2.9 21.6 + - - +
147H LYS* 5.6 8.3 - - + -
152H LYS* 4.8 22.5 - - + +
135L LYS* 6.2 0.2 - - - -
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Residues in contact with GLU 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H GLU 3.2 7.3 - - - +
97H ARG 3.2 15.2 + - - +
98H LEU 4.3 2.0 - - - +
100H GLU* 1.4 76.8 - - - +
102H THR* 1.4 57.3 + - - +
104H ASP* 3.4 11.2 + - - +
105H SER* 3.0 27.4 + - - -
204H ALA* 5.0 1.8 - - + -
205H TYR* 3.0 28.7 + - + -
124L ASP* 4.9 1.7 - - - +
135L LYS* 3.4 32.7 - - - +
82T ILE 3.1 19.3 - - - +
83T ASN* 3.2 24.4 - - - +
85T TYR 4.0 13.6 - - - +
86T GLY 4.8 4.4 + - - +
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Residues in contact with THR 102 (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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98H LEU 2.9 21.9 + - - -
99H ALA 3.5 6.5 - - - +
100H GLU 3.3 0.2 - - - -
101H GLU* 1.4 75.3 - - - +
103H LEU* 1.4 60.5 + - + +
105H SER* 3.4 3.9 + - - -
106H LEU* 3.0 35.6 + - + +
145H ILE* 6.5 0.2 - - + -
154H ILE* 4.6 8.5 - - + -
168H TRP* 3.2 19.6 - - + -
173H TRP* 3.6 33.4 - - + -
203H LEU* 3.8 15.3 - - + +
204H ALA* 5.7 0.7 - - - -
205H TYR* 3.7 11.5 - - - -
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Residues in contact with LEU 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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99H ALA* 3.4 18.1 + - + +
100H GLU* 3.3 13.7 + - - +
102H THR* 1.4 77.4 - - + +
104H ASP* 1.3 63.7 + - - +
106H LEU* 3.6 6.2 + - + +
107H ALA* 3.2 24.8 + - - +
129H SER 5.9 0.9 - - - -
130H GLY* 3.3 36.1 - - - +
132H LEU* 3.8 23.2 - - + +
145H ILE* 4.3 15.7 - - + +
147H LYS* 3.9 24.7 - - + +
154H ILE* 3.8 24.0 - - + -
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Residues in contact with ASP 104 (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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97H ARG* 5.9 1.0 + - - -
100H GLU* 2.9 23.6 + - - +
101H GLU* 3.5 10.7 - - - +
102H THR 3.3 0.2 - - - -
103H LEU* 1.3 78.7 - - - +
105H SER* 1.3 60.7 - - - +
107H ALA* 3.6 5.1 + - - +
108H GLU* 3.2 17.3 + - - +
129H SER* 6.2 0.5 - - - -
135L LYS* 5.4 4.9 - - - -
86T GLY 2.9 27.7 - - - +
87T ASN* 4.3 13.6 + - - +
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Residues in contact with SER 105 (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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101H GLU 3.0 17.7 + - - -
102H THR 3.8 3.8 - - - -
104H ASP* 1.3 74.7 - - - +
106H LEU* 1.4 59.1 + - - +
108H GLU* 3.4 2.4 + - - +
109H PHE* 3.0 31.4 + - - +
203H LEU* 3.5 36.3 + - - +
204H ALA* 4.2 5.2 - - - -
85T TYR* 3.6 26.2 + - - +
86T GLY 3.4 9.6 - - - -
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Residues in contact with LEU 106 (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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102H THR* 3.0 25.9 + - + +
103H LEU* 3.8 6.5 - - + +
104H ASP 3.4 0.2 - - - -
105H SER* 1.4 74.1 - - - +
107H ALA* 1.3 56.5 + - - +
109H PHE* 3.5 3.4 + - - +
110H PHE* 3.0 53.6 + - + -
132H LEU* 4.0 12.8 - - + -
145H ILE* 4.0 27.6 - - + -
173H TRP* 6.2 1.3 - - + -
182H LEU* 4.8 4.5 - - + -
183H HIS* 4.4 7.4 - - + -
186H LEU* 4.3 15.7 - - + -
200H LEU* 4.0 24.0 - - + -
203H LEU* 3.6 20.1 - - + +
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Residues in contact with ALA 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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103H LEU 3.2 16.0 + - - +
104H ASP* 3.7 6.5 - - - +
106H LEU* 1.3 77.4 - - - +
108H GLU* 1.3 62.9 + - - +
110H PHE* 3.5 5.4 + - - +
111H GLU* 3.1 32.2 + - - +
125H VAL* 4.3 6.6 - - + +
127H PHE* 5.5 8.1 - - + -
132H LEU* 3.7 22.4 - - + +
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Residues in contact with GLU 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ASP 3.2 5.5 + - - +
105H SER* 3.7 3.6 - - - +
106H LEU 3.3 0.2 - - - -
107H ALA* 1.3 77.7 - - - +
109H PHE* 1.4 62.4 + - - +
111H GLU* 3.3 27.5 + - - +
112H ASP* 3.0 28.6 + - - +
85T TYR* 4.0 13.0 - - + -
86T GLY 3.5 19.3 - - - +
87T ASN 3.3 17.6 + - - +
88T PRO* 3.2 28.1 - - - +
293T SER 4.8 2.3 - - - +
294T GLY* 4.8 0.5 - - - -
295T THR* 3.1 34.4 + - - +
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Residues in contact with PHE 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H SER* 3.0 18.3 + - - +
106H LEU* 3.7 6.1 - - - +
108H GLU* 1.4 74.3 - - - +
110H PHE* 1.4 60.8 + - - +
112H ASP* 3.2 14.4 + - + +
113H LEU* 3.1 30.9 + - + +
199H ASP* 4.0 20.2 - - + -
200H LEU* 3.5 26.9 - - + -
202H SER* 3.5 44.4 - - - +
203H LEU* 4.9 8.5 - - + -
85T TYR* 5.1 15.7 - + - -
299T PRO* 5.2 15.3 - - + -
300T LEU* 5.9 7.6 - - + -
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Residues in contact with PHE 110 (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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106H LEU* 3.0 43.2 + - + +
107H ALA 3.6 5.8 - - - +
109H PHE* 1.4 73.5 - - - +
111H GLU* 1.4 59.1 + - - +
113H LEU* 3.4 15.1 + - + +
114H ALA* 3.0 29.1 + - - +
123H TYR* 3.1 27.9 - - - -
125H VAL* 3.9 20.4 - - + +
132H LEU* 3.8 18.2 - - + -
134H VAL* 3.7 26.7 - - + -
145H ILE* 4.5 1.8 - - + -
186H LEU* 4.1 15.3 - - + -
190H LEU* 4.7 12.6 - - + -
200H LEU* 3.6 29.2 - - + -
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Residues in contact with GLU 111 (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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107H ALA* 3.1 23.6 + - - +
108H GLU* 3.3 32.0 + - - +
110H PHE* 1.4 74.0 - - - +
112H ASP* 1.4 61.0 + - - +
114H ALA* 3.3 7.4 + - - +
115H ASP* 2.9 28.9 + - - +
125H VAL* 4.7 7.0 - - + -
127H PHE* 3.8 34.8 - - + -
88T PRO* 5.7 2.6 - - - +
293T SER* 3.9 20.3 - - - +
294T GLY* 5.3 1.4 - - - -
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Residues in contact with ASP 112 (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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108H GLU* 3.0 23.8 + - - +
109H PHE* 3.2 15.7 + - + +
111H GLU* 1.4 76.2 - - - +
113H LEU* 1.4 60.9 + - + +
115H ASP* 3.1 26.6 - - - +
116H LYS* 3.5 13.1 - - - +
85T TYR* 5.2 6.4 - - - -
292T ARG* 3.4 18.4 + - - +
293T SER 5.6 0.3 - - - +
295T THR* 3.1 33.7 + - - +
297T PRO* 3.7 23.0 - - + +
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Residues in contact with LEU 113 (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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109H PHE* 3.1 23.8 + - + +
110H PHE* 3.6 18.8 - - + +
112H ASP* 1.4 75.4 - - + +
114H ALA* 1.4 60.2 + - - +
116H LYS* 3.5 31.8 - - - +
119H THR* 3.1 29.7 + - + +
123H TYR* 5.4 3.1 - - + +
190H LEU* 6.2 0.7 - - + -
198H LEU* 4.0 27.1 - - + -
199H ASP* 3.4 28.7 - - + +
200H LEU* 3.8 26.2 - - + -
264T GLY 5.7 1.3 - - - +
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Residues in contact with ALA 114 (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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110H PHE 3.0 17.4 + - - +
111H GLU* 3.3 8.3 + - - +
113H LEU* 1.4 72.4 - - - +
115H ASP* 1.3 66.5 + - - +
116H LYS 3.1 2.6 - - - +
119H THR* 3.1 17.9 + - - -
120H PHE 5.5 0.5 - - - +
123H TYR* 3.7 32.2 - - + +
124H ASP* 6.1 0.2 - - - -
125H VAL* 4.2 9.6 - - + +
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Residues in contact with ASP 115 (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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111H GLU* 2.9 20.7 + - - +
112H ASP* 3.1 12.6 - - - +
114H ALA* 1.3 78.8 - - - +
116H LYS* 1.3 65.0 + - - +
117H PRO* 3.8 2.6 - - - +
291T MET* 3.9 34.3 - - - +
292T ARG* 3.2 53.6 + - - +
293T SER 4.9 1.0 + - - +
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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