Contacts of the helix formed by residues 138 - 147 (chain S) in PDB entry 2DFS
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 TYR 138 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90S ARG* 3.5 45.3 - - + +
93S ASP* 2.6 36.2 + - + +
96S GLY* 4.7 4.3 - - - -
98S GLY* 3.2 39.5 + - - -
99S TYR 3.3 18.8 - - - -
100S ILE* 3.9 17.9 - - + -
136S VAL* 3.2 3.7 + - + -
137S ASN* 1.3 71.0 - - - +
139S GLU* 1.3 69.2 + - + +
141S PHE* 3.8 7.0 - - - +
142S VAL* 3.0 32.8 + - + +
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Residues in contact with GLU 139 (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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98S GLY* 4.4 1.1 + - - +
137S ASN* 3.0 9.6 + - - +
138S TYR* 1.3 85.0 - - + +
140S GLU* 1.3 63.7 + - - +
142S VAL* 3.1 26.8 - - + +
143S GLN* 3.2 26.5 + - + +
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Residues in contact with GLU 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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137S ASN* 3.0 43.4 + - + +
139S GLU* 1.3 76.6 - - - +
141S PHE* 1.3 55.8 + - - +
143S GLN* 2.8 32.1 + - + +
144S MET* 2.9 49.5 + - + +
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Residues in contact with PHE 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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897M TYR* 3.4 26.9 - + - -
90S ARG* 3.3 20.6 - - - -
105S LEU* 3.8 30.7 - - + -
124S MET* 4.2 17.5 - - + -
125S ILE* 5.6 0.7 - - + -
128S ALA* 3.4 32.1 - - + -
129S ASP 5.2 0.9 - - - -
136S VAL* 3.4 23.1 - - + -
137S ASN 3.1 18.7 + - - +
138S TYR* 3.8 7.0 - - - +
139S GLU 3.4 0.2 - - - -
140S GLU* 1.3 76.8 - - - +
142S VAL* 1.4 60.2 + - - +
144S MET* 3.6 12.9 + - + +
145S MET* 3.2 35.4 + - + +
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Residues in contact with VAL 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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86S ARG 4.0 16.4 - - - +
87S GLU* 5.2 1.3 - - - -
88S ALA* 3.3 30.7 - - + +
90S ARG* 3.3 24.7 - - + +
138S TYR* 3.0 17.8 + - + +
139S GLU* 3.1 31.0 - - + +
141S PHE* 1.4 71.0 - - - +
143S GLN* 1.3 65.0 + - + +
145S MET* 3.4 8.4 + - + +
146S THR* 2.8 32.2 + - + +
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Residues in contact with GLN 143 (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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86S ARG 5.3 0.7 - - - +
139S GLU* 3.2 27.7 + - + +
140S GLU* 2.8 38.2 + - + +
142S VAL* 1.3 77.5 - - + +
144S MET* 1.3 55.7 + - - +
146S THR* 3.3 7.2 + - - -
147S ALA* 2.9 31.3 + - - +
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Residues in contact with MET 144 (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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900M MET* 4.1 8.1 - - - +
127S GLU* 4.4 22.4 - - + +
128S ALA* 4.4 6.7 - - - -
129S ASP* 3.3 46.2 - - + +
140S GLU* 2.9 38.7 + - + +
141S PHE* 3.8 14.6 - - - +
143S GLN* 1.3 72.9 - - + +
145S MET* 1.4 60.3 + - - +
146S THR 3.3 1.0 + - - -
147S ALA* 3.3 19.1 + - - +
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Residues in contact with MET 145 (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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893M LEU* 3.5 32.1 - - + +
896M CYS* 5.5 6.9 - - + +
897M TYR* 3.6 31.6 - - + -
900M MET* 3.5 30.2 - - + +
90S ARG* 3.7 12.6 - - - +
124S MET* 5.2 12.6 - - + -
127S GLU* 5.1 5.6 - - - +
141S PHE* 3.2 45.2 + - + +
142S VAL* 3.6 13.5 - - - +
143S GLN 3.4 0.2 - - - -
144S MET* 1.4 78.4 - - - +
146S THR* 1.3 67.7 + - + +
147S ALA 3.5 0.2 - - - -
148S LYS* 6.1 0.7 - - - -
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Residues in contact with THR 146 (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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893M LEU* 5.8 3.8 - - + -
896M CYS* 6.1 4.0 - - + -
900M MET* 5.1 0.2 - - - -
42S ASN* 6.1 2.0 - - - +
85S ILE* 3.7 13.9 - - + +
86S ARG* 3.6 42.4 + - - +
87S GLU 5.9 0.2 - - - -
142S VAL* 2.8 22.4 + - + +
143S GLN* 3.3 9.4 + - - -
145S MET* 1.3 88.1 - - + +
147S ALA* 1.3 64.6 + - - +
148S LYS* 3.3 15.9 + - - +
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Residues in contact with ALA 147 (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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900M MET* 3.6 15.1 - - - +
143S GLN 2.9 17.2 + - - +
144S MET* 3.3 14.6 + - - +
146S THR* 1.3 71.5 - - - +
148S LYS* 1.3 64.8 + - - +
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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