Contacts of the helix formed by residues 129 - 142 (chain S) in PDB entry 6D84
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 LYS 129 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234G GLU* 4.1 18.8 - - + +
93S LYS* 4.2 27.8 - - - +
127S SER* 2.9 7.1 + - - +
128S LYS* 1.3 80.5 - - + +
130S ILE* 1.3 64.8 + - + +
131S ALA 3.3 1.6 - - - -
132S VAL* 3.3 4.7 - - + +
133S LYS* 2.9 48.3 + - + +
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Residues in contact with ILE 130 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G TYR* 6.1 1.1 - - + -
155G LYS* 4.2 9.2 - - - +
187G ASN* 4.0 20.0 - - - +
234G GLU* 4.9 10.1 - - - +
235G HIS* 5.0 3.6 - - - +
125S GLU* 3.3 34.3 - - - +
127S SER* 2.9 14.4 + - - +
129S LYS* 1.3 78.6 - - + +
131S ALA* 1.3 57.9 + - - +
133S LYS* 3.7 24.8 - - - +
134S ALA* 2.8 31.6 + - + +
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Residues in contact with ALA 131 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G LYS* 5.4 2.2 - - - +
90S LEU* 4.4 15.7 - - + -
113S ILE* 6.6 0.2 - - + -
116S GLU* 4.2 20.4 - - + +
117S PHE* 5.2 5.4 - - + -
125S GLU* 4.0 26.6 - - + +
127S SER 4.0 8.8 + - - +
129S LYS 3.3 0.6 - - - -
130S ILE* 1.3 76.6 - - - +
132S VAL* 1.3 60.2 + - - +
134S ALA* 3.3 5.7 + - - +
135S ILE* 2.9 29.6 + - - +
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Residues in contact with VAL 132 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90S LEU* 3.7 40.4 - - + +
93S LYS* 3.7 31.4 - - + -
94S TYR* 4.6 11.4 - - + +
113S ILE* 5.6 3.4 - - + -
128S LYS 3.4 18.8 + - - +
129S LYS* 3.3 17.3 - - + +
131S ALA* 1.3 72.2 - - - +
133S LYS* 1.3 60.0 + - - +
135S ILE* 3.3 9.5 - - + +
136S GLU* 2.9 41.5 + - - +
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Residues in contact with LYS 133 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129S LYS* 2.9 37.0 + - + +
130S ILE* 3.7 26.6 - - - +
132S VAL* 1.3 78.2 - - - +
134S ALA* 1.3 57.6 + - - +
136S GLU* 3.4 10.6 + - - +
137S ASP* 2.9 46.7 + - - +
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Residues in contact with ALA 134 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G PHE* 3.2 15.6 - - + -
152G TYR* 3.7 33.2 - - + +
155G LYS* 5.3 2.0 - - - +
116S GLU* 5.1 4.7 - - + +
130S ILE* 2.8 20.1 + - + +
131S ALA* 3.3 6.5 + - - +
133S LYS* 1.3 77.6 - - - +
135S ILE* 1.3 57.4 + - - +
137S ASP* 3.2 9.2 + - - +
138S SER* 2.9 23.4 + - - -
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Residues in contact with ILE 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G ARG* 5.1 4.0 - - - +
94S TYR* 3.7 31.8 + - + +
109S LYS* 4.3 2.2 - - + +
112S PHE* 3.6 22.4 - - + +
113S ILE* 3.5 44.0 - - + +
116S GLU* 4.7 13.6 - - + +
131S ALA 2.9 16.6 + - - +
132S VAL* 3.3 17.3 - - + +
134S ALA* 1.3 77.4 - - - +
136S GLU* 1.3 60.9 + - - +
138S SER* 2.8 25.6 + - - +
139S ASP* 2.9 16.1 + - - +
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Residues in contact with GLU 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93S LYS* 4.7 8.7 - - - +
94S TYR* 3.6 29.1 - - + +
132S VAL* 2.9 26.0 + - - +
133S LYS* 3.8 8.9 - - - +
135S ILE* 1.3 75.7 - - - +
137S ASP* 1.3 60.0 + - - +
139S ASP* 3.7 7.3 - - - +
140S MET* 2.9 26.2 + - - +
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Residues in contact with ASP 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G PHE* 3.8 20.2 - - + -
133S LYS* 2.9 39.1 + - - +
134S ALA* 3.2 8.2 + - - +
136S GLU* 1.3 79.0 - - - +
138S SER* 1.3 59.8 + - - +
140S MET* 3.2 11.7 + - - +
141S LEU* 3.0 24.3 + - - +
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Residues in contact with SER 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G PHE* 3.2 26.9 - - - -
83G ARG* 3.3 32.7 + - - -
117G PHE* 3.7 19.9 - - - -
116S GLU* 5.8 2.3 - - - +
134S ALA 2.9 12.6 + - - -
135S ILE* 2.8 33.3 + - - +
137S ASP* 1.3 73.2 - - - +
139S ASP* 1.3 63.3 + - - +
141S LEU* 3.3 3.7 + - - +
142S GLN* 3.2 9.2 + - - -
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Residues in contact with ASP 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G ARG* 6.2 0.4 - - - +
94S TYR* 3.1 23.6 + - + +
109S LYS* 3.9 13.6 + - - -
135S ILE* 2.9 19.1 + - + +
136S GLU* 3.8 8.7 - - + +
138S SER* 1.3 76.0 + - - +
140S MET* 1.3 58.1 + - - +
142S GLN* 3.0 29.4 + - - +
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Residues in contact with MET 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136S GLU 2.9 19.1 + - - +
137S ASP* 3.2 15.9 + - - +
139S ASP* 1.3 74.4 - - - +
141S LEU* 1.3 58.0 + - - +
142S GLN* 2.9 13.7 + - - +
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Residues in contact with LEU 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G PHE* 3.5 39.3 - - + -
115G THR* 3.8 32.1 - - + +
117G PHE* 4.6 9.2 - - + -
137S ASP 3.0 11.0 + - - +
138S SER* 3.3 10.1 + - - +
139S ASP 3.2 0.6 - - - -
140S MET* 1.3 75.5 - - - +
142S GLN* 1.3 83.6 + - - +
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Residues in contact with GLN 142 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G PHE* 3.2 29.0 + - - +
80G THR* 3.4 25.4 - - - +
138S SER 3.2 10.0 + - - -
139S ASP* 3.0 23.3 + - - +
140S MET* 2.9 26.7 + - - +
141S LEU* 1.3 91.8 + - - +
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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