Contacts of the helix formed by residues 113 - 129 (chain H) in PDB entry 5A31
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 SER 113 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F HIS* 3.2 35.9 - - - -
69H PRO* 4.8 5.7 + - - +
70H GLN* 5.5 1.6 + - - -
73H TYR* 5.2 3.1 - - - +
110H PHE* 3.2 26.6 + - - +
112H ASP* 1.3 78.8 - - - +
114H ALA* 1.3 63.8 + - - +
115H CYS 3.3 1.6 + - - -
116H PHE* 3.4 16.2 + - - +
117H THR* 3.3 24.2 + - - +
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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
----------------------------------------------------------
106H ILE 4.4 0.7 - - - +
107H VAL* 3.8 31.9 - - + +
110H PHE* 3.8 8.7 - - + +
111H GLY 3.0 21.1 + - - +
112H ASP 3.0 1.8 + - - -
113H SER* 1.3 78.1 + - - +
115H CYS* 1.3 63.4 + - - +
117H THR* 2.6 23.9 + - - +
118H LEU* 3.0 17.2 + - + +
144H LEU* 4.3 11.0 - - + -
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Residues in contact with CYS 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F GLN* 5.0 1.6 - - - -
112H ASP 4.0 10.2 + - - +
114H ALA* 1.3 79.3 - - - +
116H PHE* 1.3 108.4 - - - +
118H LEU* 3.2 0.7 + - - +
119H SER* 3.0 19.2 + - - -
141H SER* 3.4 21.8 - - - +
144H LEU* 3.7 32.5 - - + +
145H ASN* 4.2 18.8 - - - +
148H LEU* 4.0 16.6 - - + -
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Residues in contact with PHE 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ALA 4.8 1.6 - - - -
14F GLN* 3.7 26.9 - - + -
15F ALA* 3.4 43.3 - - + -
18F HIS* 3.5 34.8 - + + -
20F ALA* 3.8 20.4 - - + -
23F ASP* 4.7 0.7 - - - -
73H TYR* 4.1 19.1 + - + +
113H SER* 3.4 12.5 + - - +
114H ALA 3.3 0.2 - - - -
115H CYS* 1.3 96.5 - - - +
117H THR* 1.3 58.4 + - - +
119H SER* 3.0 10.4 + - - -
120H LEU* 2.8 27.9 + - - +
145H ASN* 6.2 0.9 - - - -
148H LEU* 3.8 27.4 - - + -
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Residues in contact with THR 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H TYR* 3.2 30.5 - - + -
92H LEU* 4.2 16.4 - - + +
106H ILE* 3.9 14.3 - - - +
110H PHE* 3.5 27.8 - - + -
113H SER* 3.3 14.6 + - - +
114H ALA* 2.6 25.6 + - - -
116H PHE* 1.3 75.8 - - - +
118H LEU* 1.3 56.4 + - - +
120H LEU* 3.5 8.6 - - - +
121H LEU* 2.9 28.5 + - - +
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Residues in contact with LEU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H HIS* 4.1 27.6 - - + +
106H ILE* 3.8 31.2 - - + -
107H VAL* 4.0 15.0 - - + -
114H ALA* 3.0 18.9 + - + +
115H CYS 3.6 2.0 - - - +
117H THR* 1.3 73.6 - - - +
119H SER* 1.3 60.9 + - - +
121H LEU* 4.1 1.3 - - + -
122H GLY* 2.8 11.6 + - - -
137H CYS* 2.8 38.1 - - - +
140H LYS* 4.2 11.9 - - + -
141H SER* 3.6 13.5 - - - +
144H LEU* 3.4 29.2 - - + -
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Residues in contact with SER 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ASP* 5.0 2.5 + - - -
115H CYS 3.0 12.9 + - - -
116H PHE* 3.2 12.6 - - - -
118H LEU* 1.3 73.8 - - - +
120H LEU* 1.3 59.8 + - - +
122H GLY 3.2 1.4 + - - -
123H HIS* 3.0 25.3 + - - +
138H TYR* 3.5 21.0 - - - -
141H SER* 3.2 15.6 + - - -
148H LEU* 5.4 3.6 - - - -
150H SER* 4.4 9.9 + - - -
151H PRO* 4.2 15.0 - - - +
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Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H TYR* 3.5 29.8 - - + +
76H ALA* 4.1 1.3 - - + -
77H LYS* 4.1 35.9 - - + +
80H VAL* 3.7 35.9 - - + -
92H LEU* 3.8 22.4 - - + -
116H PHE 2.8 12.9 + - - +
117H THR* 3.5 9.0 - - - +
119H SER* 1.3 73.8 - - - +
121H LEU* 1.3 65.0 + - - +
123H HIS* 3.0 19.9 + - + +
124H VAL* 3.1 12.7 + - + +
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Residues in contact with LEU 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H GLU* 4.3 12.3 - - + +
92H LEU* 3.9 26.5 - - + -
93H SER* 4.0 15.3 - - - +
103H HIS* 5.0 3.1 - - + -
106H ILE* 3.7 30.1 - - + -
117H THR 2.9 18.8 + - - +
118H LEU* 3.6 7.4 - - + +
119H SER 3.3 0.2 - - - -
120H LEU* 1.3 77.3 - - - +
122H GLY* 1.3 59.8 + - - +
124H VAL* 3.2 8.1 + - + +
125H TYR* 2.8 67.8 + - + +
137H CYS* 3.7 12.8 - - - -
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Residues in contact with GLY 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H LEU 2.8 15.1 + - - -
119H SER 3.6 4.3 - - - -
120H LEU 3.2 0.2 - - - -
121H LEU* 1.3 77.0 - - - +
123H HIS* 1.3 61.1 + - - +
125H TYR* 3.0 5.7 + - - +
126H CYS* 2.9 28.1 + - - -
134H GLY 4.2 5.6 - - - -
137H CYS* 3.4 18.1 - - - -
138H TYR* 3.6 13.9 - - - -
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Residues in contact with HIS 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H VAL* 4.2 25.0 - - + +
85H LEU* 5.5 0.7 - - + -
119H SER 3.0 12.0 + - - +
120H LEU* 3.0 15.9 + - + +
122H GLY* 1.3 74.7 - - - +
124H VAL* 1.3 64.7 + - - +
126H CYS* 4.1 2.3 - - - +
127H LYS* 3.2 58.5 + - + +
138H TYR* 3.1 20.0 + - + +
599H ASN* 6.3 0.4 - - - -
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Residues in contact with VAL 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H VAL* 3.9 27.6 - - + -
85H LEU* 3.8 34.8 - - + +
88H GLY 5.3 1.1 - - - -
89H GLU* 4.0 23.6 - - + +
92H LEU* 5.6 1.3 - - + -
120H LEU* 3.1 18.3 + - + +
121H LEU* 3.4 13.2 - - + +
122H GLY 3.2 0.2 - - - -
123H HIS* 1.3 78.8 - - + +
125H TYR* 1.3 50.4 + - + +
127H LYS* 3.4 5.5 + - - +
128H THR* 2.3 46.9 + - - +
130H ARG* 4.5 4.7 - - - +
473K VAL* 5.8 0.4 - - + -
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Residues in contact with TYR 125 (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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89H GLU* 3.7 9.5 + - - -
93H SER* 4.3 7.3 - - - -
103H HIS* 5.1 6.7 - + - -
121H LEU* 2.8 62.4 + - + +
122H GLY* 3.0 8.2 + - - +
124H VAL* 1.3 78.6 - - + +
126H CYS* 1.3 64.3 + - - +
128H THR* 3.1 6.9 + - - -
129H ASP 3.0 4.7 + - - -
130H ARG* 2.9 70.3 + - + +
133H LYS* 3.4 56.6 + - + -
134H GLY* 3.7 12.3 - - - -
137H CYS* 5.0 4.9 - - + -
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Residues in contact with CYS 126 (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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122H GLY 2.9 20.0 + - - +
123H HIS 4.1 3.6 - - - +
125H TYR* 1.3 75.7 - - - +
127H LYS* 1.3 62.6 + - - +
129H ASP* 3.2 10.4 + - - -
130H ARG 4.4 0.9 - - - -
131H LEU* 3.4 31.6 - - + +
134H GLY* 4.0 14.8 - - - -
135H SER 4.5 0.2 - - - -
138H TYR* 3.4 27.4 - - + +
158H ILE* 3.8 20.0 - - + -
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Residues in contact with LYS 127 (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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80H VAL* 5.6 4.9 + - - +
85H LEU* 3.8 32.3 - - + +
123H HIS* 3.2 49.8 + - + +
124H VAL 3.7 3.6 - - - +
126H CYS* 1.3 81.0 - - - +
128H THR* 1.3 60.3 + - - +
129H ASP 3.3 0.9 + - - -
599H ASN* 3.6 35.7 + - - +
476K PRO 4.9 5.2 - - - +
477K GLN* 5.2 3.5 - - - +
482K TYR* 4.4 9.7 + - - -
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Residues in contact with THR 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H LEU* 4.8 6.4 - - - +
124H VAL* 2.3 37.7 + - - +
125H TYR* 3.1 10.4 + - - -
127H LYS* 1.3 74.9 - - - +
129H ASP* 1.3 65.5 + - - +
130H ARG* 3.1 31.2 + - + +
469K ARG* 3.9 5.6 - - - +
472K LEU* 3.6 20.3 - - - +
473K VAL* 3.5 34.4 - - + +
476K PRO* 5.6 3.1 - - - -
482K TYR* 5.0 0.9 - - - -
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Residues in contact with ASP 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H TYR 3.0 2.4 + - - -
126H CYS 3.2 8.8 + - - -
127H LYS 3.1 5.3 + - - -
128H THR* 1.3 80.5 - - - +
130H ARG* 1.3 61.0 + - - +
131H LEU* 3.0 20.2 + - - +
469K ARG* 3.7 28.6 + - + +
472K LEU* 3.8 12.6 - - + -
482K TYR* 4.3 11.4 - - - +
485K ILE* 4.2 5.4 - - - +
501K TYR* 2.8 45.2 + - - -
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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
------------------------------------------------------------
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