Contacts of the strand formed by residues 94 - 102 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C GLY* 3.0 24.8 + - - +
83C LEU* 3.3 8.6 - - + -
84C VAL* 2.9 27.2 + - - +
93C ASP* 1.3 73.6 - - - +
95C CYS* 1.3 60.5 + - - +
129C PHE 3.2 6.5 - - - +
130C PHE* 3.9 27.7 - - + -
131C GLY 3.1 4.0 + - - -
132C ARG* 2.6 57.9 + - - +
133C GLN* 4.9 2.4 + - - -
1I NAG 5.6 0.4 + - - -
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Residues in contact with CYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 4.2 5.2 - - - -
84C VAL 3.1 22.9 - - - +
86C ALA* 3.2 31.4 - - - -
89C ALA* 3.3 19.5 - - + -
93C ASP 5.5 1.6 - - - -
94C ASN* 1.3 73.2 - - - +
96C VAL* 1.3 60.4 + - - +
97C PHE 3.3 4.3 + - - -
128C VAL* 3.1 7.8 - - - +
129C PHE* 2.9 45.4 + - - -
172C LEU* 4.1 13.5 - - - -
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C MET* 3.8 21.8 - - + -
75C LEU* 3.8 19.7 - - + -
79C LEU* 3.9 15.0 - - + -
83C LEU* 4.2 8.6 - - + +
84C VAL 4.6 1.8 + - - -
86C ALA* 3.7 13.1 + - - +
95C CYS* 1.3 72.0 - - - +
97C PHE* 1.3 63.9 + - - +
98C SER* 4.0 9.5 - - - +
99C VAL* 3.6 31.0 - - + -
126C ALA* 4.7 1.1 - - + -
127C ILE 3.7 5.8 - - - +
128C VAL* 3.6 20.0 - - + -
419C SER 3.9 12.0 + - - +
420C GLN* 5.8 4.0 - - + +
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Residues in contact with PHE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA* 4.5 6.5 - - + -
95C CYS* 3.3 5.0 + - - -
96C VAL* 1.3 72.6 - - - +
98C SER* 1.3 74.4 + - - +
127C ILE* 2.8 19.5 + - + +
129C PHE* 3.2 34.8 - + + -
170C PRO* 3.9 32.5 - - + -
171C VAL 5.7 0.2 - - - -
172C LEU* 3.3 28.9 - - + -
344C PHE* 3.9 25.6 - + - -
388C GLY 5.7 0.4 - - - -
389C PHE 5.9 0.2 - - - -
393C LYS* 3.6 18.2 - - - -
417C LEU* 3.7 1.6 - - + +
418C GLU* 2.8 54.0 + - + -
647C VAL* 4.8 1.8 - - + -
648C PHE* 6.2 0.7 - + - -
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C VAL* 3.3 3.3 - - - +
97C PHE* 1.3 90.3 - - - +
99C VAL* 1.3 67.6 + - - +
100C GLU* 4.2 2.7 - - - -
125C LEU 3.8 1.2 + - - +
126C ALA* 3.1 3.5 - - - +
127C ILE* 2.6 58.9 + - - +
343C ALA* 5.9 0.2 - - - -
344C PHE* 3.9 6.8 - - - -
416C LEU 3.4 7.0 - - - -
417C LEU* 3.2 25.8 - - - -
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 3.2 36.3 - - + +
71C VAL* 3.8 31.2 - - + -
72C MET* 4.5 0.4 - - + +
75C LEU* 3.7 18.2 - - + -
96C VAL* 3.6 22.4 - - + -
98C SER* 1.3 78.2 - - - +
100C GLU* 1.3 61.7 + - - +
124C ALA* 4.4 9.4 - - + -
125C LEU 3.8 3.1 - - - -
126C ALA* 3.8 5.2 - - + +
415C PHE* 5.5 0.2 - - - -
416C LEU* 3.0 32.2 + - + +
417C LEU* 5.7 1.1 - - - +
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 3.9 7.2 - - - -
68C LEU* 5.1 0.4 - - - -
98C SER* 4.2 3.8 - - - -
99C VAL* 1.3 74.8 - - - +
101C LEU* 1.3 67.3 + - + +
124C ALA* 2.8 9.5 - - - +
125C LEU* 2.7 41.9 + - + +
341C LEU 3.9 2.3 - - - +
342C GLY* 3.3 9.1 - - - -
343C ALA* 3.1 39.1 + - + +
344C PHE* 4.5 9.7 + - + -
348C ARG* 3.2 32.8 + - - +
413C TRP* 5.6 4.9 - - + -
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LEU 4.6 4.5 - - - +
60C PHE 3.7 16.4 - - - +
61C ALA 3.3 26.2 - - - +
62C ASP* 4.4 0.9 - - - -
63C LEU* 3.8 23.9 - - + +
100C GLU* 1.3 87.4 - - - +
102C GLN* 1.3 77.3 + - - +
103C LEU* 3.3 19.2 + - + +
104C PRO* 5.3 2.0 - - + -
122C ARG* 3.7 21.3 - - - +
123C GLU 2.9 28.7 - - - +
125C LEU* 4.3 1.4 - - - +
348C ARG* 4.3 18.9 + - - +
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Residues in contact with GLN 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLU 3.5 3.2 + - - -
101C LEU* 1.3 82.3 - - - +
103C LEU* 1.3 93.2 + - - +
104C PRO* 3.4 3.9 - - + +
123C GLU* 3.2 49.0 + - + +
124C ALA 3.7 6.5 - - - +
125C LEU* 3.7 23.0 - - + +
142C VAL* 4.1 6.7 - - + +
159C ARG* 3.3 37.9 + - - +
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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