Contacts of the strand formed by residues 94 - 102 (chain D) in PDB entry 2C11
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 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D LEU 5.4 6.1 + - - +
82D GLY* 3.6 21.3 + - - +
83D LEU* 3.1 14.9 - - + -
84D VAL* 2.8 25.6 + - - -
93D ASP* 1.3 70.4 - - - +
95D CYS* 1.3 59.0 + - - +
128D VAL* 5.1 0.2 - - - -
129D PHE 3.4 4.0 - - - +
130D PHE* 3.0 43.5 - - + +
132D ARG* 2.9 44.3 + - - +
133D GLN* 4.7 1.4 + - - +
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Residues in contact with CYS 95 (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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83D LEU* 3.7 2.0 - - - +
84D VAL 3.1 20.6 - - - +
86D ALA* 3.5 28.7 - - - -
89D ALA* 3.9 19.3 - - + -
90D ARG 6.0 0.2 - - - -
93D ASP 5.0 2.7 - - - -
94D ASN* 1.3 74.5 - - - +
96D VAL* 1.3 60.7 + - - +
97D PHE 4.9 0.2 - - - -
128D VAL* 3.0 8.5 - - - +
129D PHE* 2.8 64.6 + - - -
166D TYR* 5.8 0.2 - - - -
172D LEU* 4.1 6.1 - - - -
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Residues in contact with VAL 96 (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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72D MET* 3.9 21.8 - - + -
75D LEU* 4.2 13.0 - - + -
79D LEU* 4.0 13.5 - - + -
83D LEU* 3.7 33.2 - - + +
84D VAL 4.2 2.4 + - - -
86D ALA* 3.3 16.8 + - - +
95D CYS* 1.3 72.5 - - - +
97D PHE* 1.3 62.8 + - - +
98D SER 4.0 2.5 - - - +
99D VAL* 3.8 29.6 - - + -
126D ALA* 4.5 2.5 - - + -
127D ILE 3.7 11.4 - - - +
128D VAL* 4.2 3.8 - - + -
418D GLU 4.3 0.5 + - - -
419D SER 3.9 12.6 - - - +
420D GLN* 5.5 3.3 - - + +
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Residues in contact with PHE 97 (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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86D ALA* 4.3 4.9 - - - -
95D CYS* 3.6 3.8 + - - -
96D VAL* 1.3 71.3 - - - +
98D SER* 1.3 70.9 + - - +
127D ILE* 2.9 20.6 + - + +
129D PHE* 3.3 44.9 - + + -
170D PRO* 3.4 31.9 - - + -
171D VAL 5.2 0.2 - - - -
172D LEU* 3.7 7.4 - - + -
344D PHE* 3.4 30.1 - + - -
388D GLY 5.7 0.4 - - - -
389D PHE 5.6 0.4 - - - -
393D LYS* 3.1 19.3 - - - -
416D LEU 5.5 0.2 - - - -
417D LEU* 3.2 1.9 - - - +
418D GLU* 2.5 64.8 + - + +
647D VAL* 4.9 0.7 - - + -
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Residues in contact with SER 98 (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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96D VAL* 3.5 2.1 - - - +
97D PHE* 1.3 89.5 - - - +
99D VAL* 1.3 62.1 + - - +
100D GLU* 6.1 1.6 - - - -
125D LEU 4.1 2.1 + - - -
126D ALA* 2.8 11.8 - - - +
127D ILE* 2.8 58.1 + - - +
344D PHE* 4.0 10.2 - - - -
416D LEU 3.5 7.2 - - - -
417D LEU* 3.5 20.9 - - - -
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Residues in contact with VAL 99 (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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63D LEU* 4.1 6.1 - - + -
68D LEU* 3.5 18.2 - - + +
71D VAL* 3.4 32.3 - - + -
72D MET* 4.7 2.0 - - + -
75D LEU* 4.3 8.7 - - + -
96D VAL* 3.8 15.9 - - + -
98D SER* 1.3 81.9 - - - +
100D GLU* 1.3 63.9 + - - +
124D ALA* 4.1 11.9 - - + -
125D LEU 3.3 6.1 - - - +
126D ALA* 3.5 15.7 - - + -
416D LEU* 3.1 39.0 + - + +
417D LEU* 4.7 1.3 - - - +
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Residues in contact with GLU 100 (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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62D ASP* 4.8 0.5 - - - +
63D LEU* 3.2 13.1 - - - +
68D LEU* 4.6 2.2 - - - -
98D SER* 6.1 1.6 - - - +
99D VAL* 1.3 76.0 - - - +
101D LEU* 1.3 68.9 + - - +
124D ALA* 3.1 8.1 - - - -
125D LEU* 3.0 38.5 + - + +
341D LEU 4.0 1.9 - - - +
342D GLY* 3.8 2.8 - - - -
343D ALA* 2.9 46.7 + - + +
344D PHE* 4.1 10.4 + - + -
348D ARG* 3.4 28.3 + - - -
413D TRP* 5.6 2.1 - - + -
417D LEU* 5.4 2.0 - - + -
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Residues in contact with LEU 101 (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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59D LEU 4.7 3.1 - - - +
60D PHE* 4.1 15.5 - - + +
61D ALA 3.9 20.6 - - - +
62D ASP* 4.1 6.5 - - - +
63D LEU* 3.3 25.2 - - + +
100D GLU* 1.3 90.7 + - - +
102D GLN* 1.3 80.0 + - - +
103D LEU* 3.6 27.1 + - + +
104D PRO* 5.2 2.0 - - + -
122D ARG* 3.3 32.1 - - - +
123D GLU 3.8 8.5 - - - +
125D LEU* 4.6 2.0 - - - +
348D ARG* 4.2 14.4 + - - +
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Residues in contact with GLN 102 (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 GLU 3.4 0.8 + - - -
101D LEU* 1.3 82.7 - - - +
103D LEU* 1.3 94.3 + - - +
104D PRO* 3.5 2.6 - - - +
123D GLU* 3.2 42.6 + - + +
124D ALA* 3.7 7.6 - - - +
125D LEU* 3.5 25.0 - - - +
142D VAL* 3.9 19.7 - - + -
159D ARG* 3.1 28.3 + - - +
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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