Contacts of the strand formed by residues 137 - 146 (chain D) in PDB entry 6CET
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 ILE 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D PHE* 5.3 0.9 - - + -
107D GLN* 3.3 17.9 - - - +
109D ILE* 4.5 20.4 - - + -
113D ASP* 5.1 13.2 - - + +
117D LEU* 3.7 41.9 - - + +
133D GLU* 3.3 5.4 - - - +
134D PHE* 2.9 39.6 + - + +
135D ALA* 4.5 8.5 - - + +
136D GLY* 1.3 80.6 - - - +
138D ARG* 1.3 68.3 + - - +
1394D THR* 6.4 1.3 - - - -
1396D ALA* 3.8 26.2 - - + +
1397D VAL* 6.5 0.4 - - + -
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Residues in contact with ARG 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PHE* 3.2 25.7 - - - -
105D LYS* 3.6 24.9 + - - +
106D ASP* 3.8 11.9 + - - +
107D GLN* 3.4 30.0 + - - +
117D LEU* 6.0 0.9 - - - -
131D LYS* 3.5 33.5 - - - +
132D VAL 3.4 4.7 - - - -
133D GLU* 4.8 2.7 - - + -
136D GLY 4.7 5.4 + - - +
137D ILE* 1.3 87.2 - - - +
139D ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LEU* 3.6 29.6 - - + -
103D THR 4.1 6.3 - - - -
104D PHE* 4.5 2.9 - - + +
117D LEU* 5.4 8.5 - - + -
130D GLN 3.7 0.6 - - - +
131D LYS* 3.4 7.6 - - - +
132D VAL* 2.9 50.2 + - + +
138D ARG* 1.3 79.2 - - - +
140D GLN* 1.3 62.4 + - - +
141D ALA 4.3 0.4 - - - -
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Residues in contact with GLN 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LEU* 3.8 2.9 - - - +
103D THR* 2.8 53.1 + - - +
105D LYS* 4.4 18.2 - - - +
129D THR* 5.0 15.5 + - - +
130D GLN 3.4 10.5 - - - +
131D LYS* 5.0 7.6 - - + +
139D ALA* 1.3 76.2 - - - +
141D ALA* 1.3 68.7 + - - +
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Residues in contact with ALA 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 5.7 4.5 - - + -
101D GLU 3.8 8.1 - - - +
102D LEU* 3.8 6.5 - - + -
103D THR* 5.1 1.7 + - - +
126D ALA* 6.3 2.7 - - + -
127D TYR 4.1 13.0 - - - +
128D ILE* 5.1 0.6 - - - +
129D THR* 4.2 13.5 + - - +
130D GLN* 2.9 32.7 + - + +
132D VAL* 6.2 1.1 - - + +
139D ALA 4.3 0.2 - - - -
140D GLN* 1.3 83.1 - - - +
142D GLY* 1.3 59.5 + - - +
144D LEU* 5.7 2.7 - - + -
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Residues in contact with GLY 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D GLU* 2.6 57.8 + - - +
103D THR* 6.4 0.2 - - - -
128D ILE* 4.1 13.9 - - - +
141D ALA* 1.3 78.4 - - - +
143D GLU* 1.3 57.9 + - - -
144D LEU* 3.7 6.1 - - - +
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Residues in contact with GLU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 3.7 12.1 - - + +
100D VAL 3.8 0.5 - - - -
101D GLU* 3.4 29.6 + - + +
128D ILE* 4.2 3.0 - - - +
142D GLY* 1.3 75.6 - - - +
144D LEU* 1.3 59.3 + - - +
145D TRP* 2.4 43.7 + - + +
150D LYS* 3.5 27.5 + - - +
745D LYS* 4.8 22.1 - - + +
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 3.7 33.8 - - + +
99D LEU 3.0 10.8 - - - +
100D VAL* 3.7 19.3 - - + -
126D ALA* 4.0 25.1 - - + +
127D TYR 5.2 2.0 - - - +
128D ILE* 3.7 33.0 - - + +
141D ALA* 5.7 1.6 - - + -
142D GLY* 4.4 5.6 - - - +
143D GLU* 1.3 76.5 - - - +
145D TRP* 1.3 59.5 + - - +
150D LYS* 3.3 11.0 - - - +
151D VAL* 3.1 51.2 + - - +
152D MET 4.5 4.7 - - - +
154D GLY 4.9 1.3 - - - +
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Residues in contact with TRP 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 3.9 3.4 - - - -
98D ASP* 2.8 23.4 + - - +
99D LEU* 2.9 54.6 + - + +
143D GLU* 2.4 39.3 + - + +
144D LEU* 1.3 75.4 - - - +
146D VAL* 1.3 58.8 + - - +
147D LYS 4.8 3.1 - - - +
148D ASN 3.8 14.6 - - - -
149D GLU* 3.2 30.5 - - - -
150D LYS* 3.6 27.4 - - + -
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Residues in contact with VAL 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D VAL* 5.7 4.5 - - + -
96D THR 3.7 22.0 - - - +
97D LEU* 4.3 11.4 - - + -
98D ASP* 3.5 4.7 - - - -
145D TRP* 1.3 73.2 - - - +
147D LYS* 1.3 74.0 + - + +
148D ASN 2.7 17.8 + - - -
149D GLU* 2.9 33.5 + - + +
151D VAL* 3.6 34.5 - - + -
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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