Contacts of the helix formed by residues 114 - 128 (chain H) in PDB entry 2WWB
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 ASN 114 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H LYS* 3.0 39.4 + - - +
113H VAL* 1.4 74.0 - - - +
115H HIS* 1.3 67.0 + - + +
116H ASN* 3.4 12.1 - - - +
117H GLU* 3.2 45.1 + - + +
118H LYS* 3.1 29.6 + - - +
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Residues in contact with HIS 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H VAL 4.4 11.5 + - - -
114H ASN* 1.3 80.1 + - - +
116H ASN* 1.4 64.9 + - - +
118H LYS* 3.8 4.5 + - - +
119H ARG* 3.1 40.7 + - - +
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Residues in contact with ASN 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H ASN* 3.8 12.0 - - - +
115H HIS* 1.4 80.5 + - - +
117H GLU* 1.4 88.1 + - - +
119H ARG* 3.3 26.9 + - - +
120H TYR* 3.0 48.6 + - + -
265H GLU* 4.9 0.7 - - - +
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Residues in contact with GLU 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H VAL* 5.5 0.9 - - - +
111H VAL* 6.1 1.4 - - - +
112H LYS 5.6 1.4 - - - +
114H ASN* 3.2 40.4 + - + +
115H HIS 3.5 0.4 - - - -
116H ASN* 1.4 94.9 + - - +
118H LYS* 1.4 60.1 + - - +
120H TYR* 3.5 11.2 + - + +
121H ALA* 3.0 28.2 + - - +
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Residues in contact with LYS 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H VAL* 5.0 15.7 - - + -
114H ASN 3.1 19.8 + - - +
115H HIS* 4.1 4.7 - - - +
117H GLU* 1.4 77.0 - - - +
119H ARG* 1.4 58.8 + - + +
121H ALA* 3.4 7.8 + - + +
122H THR* 3.1 48.2 + - + +
233H LEU 5.9 2.0 + - - -
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Residues in contact with ARG 119 (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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115H HIS* 3.1 25.1 + - - +
116H ASN* 3.3 38.9 + - - +
118H LYS* 1.4 77.8 - - + +
120H TYR* 1.4 61.1 + - - +
122H THR* 3.2 18.6 + - - +
123H ALA* 3.2 15.9 + - - +
263H GLY* 5.2 3.7 - - - -
264H SER* 2.9 47.8 + - - +
265H GLU* 3.4 31.2 + - + +
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Residues in contact with TYR 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ILE* 5.8 6.1 - - + -
116H ASN* 3.0 44.3 + - + +
117H GLU* 3.7 10.8 - - + +
118H LYS 3.4 0.2 - - - -
119H ARG* 1.4 74.8 - - - +
121H ALA* 1.4 57.3 + - - +
123H ALA* 3.4 5.4 + - + +
124H SER* 3.0 33.0 + - - -
265H GLU* 3.1 41.1 + - + -
266H THR 5.9 1.6 - - - -
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Residues in contact with ALA 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ILE* 5.0 4.0 - - - -
38H VAL* 3.7 40.4 - - + -
117H GLU 3.0 18.2 + - - +
118H LYS* 3.5 10.5 - - + +
120H TYR* 1.4 73.9 - - - +
122H THR* 1.4 63.7 + - + +
124H SER* 3.2 16.2 + - - -
125H ALA* 3.2 15.8 + - - +
235H LEU* 4.4 6.8 - - + +
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Residues in contact with THR 122 (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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118H LYS* 3.1 37.7 + - + +
119H ARG* 3.2 18.9 + - - +
121H ALA* 1.4 75.7 - - + +
123H ALA* 1.4 56.4 + - - +
125H ALA* 3.3 7.3 + - - +
126H ILE* 3.0 43.9 + - - +
233H LEU* 4.8 17.7 - - + +
234H ASN* 5.9 3.4 - - - -
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Residues in contact with ALA 123 (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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25H VAL* 4.0 16.3 - - + +
28H ALA* 5.2 2.0 - - - +
119H ARG 3.2 19.7 + - - +
120H TYR* 3.8 7.9 - - + +
122H THR* 1.4 76.2 + - - +
124H SER* 1.4 55.6 + - - +
126H ILE* 3.5 10.6 + - - +
127H ALA* 3.1 26.7 + - - +
265H GLU* 5.2 10.8 - - + -
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Residues in contact with SER 124 (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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28H ALA* 5.1 7.9 - - - -
29H PRO 5.6 4.9 - - - -
30H ILE* 5.7 3.1 - - - +
31H ARG* 5.7 10.8 + - - -
34H ILE* 4.2 18.9 - - - +
35H VAL* 5.5 6.8 + - - +
120H TYR 3.0 20.2 + - - -
121H ALA* 3.2 13.7 + - - -
123H ALA* 1.4 72.8 - - - +
125H ALA* 1.4 58.8 + - - +
127H ALA* 3.4 8.3 + - - +
128H ALA* 3.0 26.0 + - - +
235H LEU* 5.8 0.3 - - - +
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Residues in contact with ALA 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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35H VAL* 5.0 2.7 - - - -
121H ALA 3.2 20.2 + - - +
122H THR* 3.5 8.3 - - - +
124H SER* 1.4 75.3 + - - +
126H ILE* 1.4 63.0 + - - +
128H ALA* 3.2 20.5 + - - +
129H THR* 3.5 6.9 + - - +
234H ASN 5.9 0.4 - - - -
235H LEU* 3.5 33.8 - - + +
238H LEU* 3.5 22.5 - - + +
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Residues in contact with ILE 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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25H VAL* 3.9 18.8 - - + +
26H PHE* 3.4 38.7 - - + -
122H THR* 3.0 31.0 + - - +
123H ALA* 3.7 5.4 - - - +
124H SER 3.4 0.2 - - - -
125H ALA* 1.4 73.6 - - - +
127H ALA* 1.4 60.6 + - - +
129H THR* 2.8 24.1 + - - +
130H ALA 4.1 0.2 + - - -
230H VAL 6.1 0.4 - - - +
233H LEU* 5.3 14.8 - - + -
238H LEU* 4.3 14.1 - - + -
250H TRP* 5.3 10.1 - - + -
258H LEU* 3.9 29.4 - - + -
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Residues in contact with ALA 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H VAL 3.8 9.2 - - - +
26H PHE* 3.8 13.1 - - - +
27H SER 3.8 8.1 - - - +
28H ALA* 3.7 35.0 - - + +
29H PRO 5.7 0.9 - - - +
30H ILE* 5.2 4.1 - - - +
123H ALA 3.1 16.6 + - - +
124H SER 3.7 5.8 - - - +
125H ALA 3.3 0.2 - - - -
126H ILE* 1.4 75.9 - - - +
128H ALA* 1.4 60.1 + - - +
129H THR 3.3 0.2 - - - -
130H ALA* 3.4 17.5 + - - +
131H VAL* 4.5 4.9 - - - +
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Residues in contact with ALA 128 (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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30H ILE* 3.7 32.8 - - + +
35H VAL* 5.1 10.8 - - + -
124H SER 3.0 13.4 + - - +
125H ALA* 3.2 16.5 + - - +
127H ALA* 1.4 76.5 - - - +
129H THR* 1.4 59.4 + - + +
130H ALA 3.2 1.9 + - - -
131H VAL* 3.6 13.9 - - - +
235H LEU* 6.0 0.9 - - + -
244H LEU* 5.2 6.3 - - + -
245H GLY* 4.7 13.1 + - - +
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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