Contacts of the strand formed by residues 94 - 102 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU 5.4 6.5 + - - +
82B GLY* 3.9 17.3 + - - +
83B LEU* 3.2 14.2 - - + -
84B VAL* 2.7 33.3 + - - +
93B ASP* 1.3 71.5 - - - +
95B CYS* 1.3 54.2 + - - +
129B PHE 3.4 4.0 - - - +
130B PHE* 2.9 45.6 - - + +
132B ARG* 2.8 45.2 + - - +
133B GLN* 5.4 1.0 + - - -
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Residues in contact with CYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.7 2.9 - - - +
84B VAL* 3.1 27.4 - - + +
86B ALA* 3.5 31.2 - - - -
89B ALA* 3.8 11.7 - - - -
90B ARG 5.9 0.2 - - - -
93B ASP 4.8 2.7 - - - -
94B ASN* 1.3 73.0 - - - +
96B VAL* 1.3 59.0 + - - +
97B PHE 3.4 1.6 + - - -
128B VAL* 3.3 6.1 - - - +
129B PHE* 2.8 58.6 + - - -
172B LEU* 4.3 6.1 - - - -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 3.9 20.9 - - + -
75B LEU* 4.2 13.7 - - + -
79B LEU* 3.9 18.4 - - + -
83B LEU* 3.8 28.7 - - + +
84B VAL 4.2 3.2 + - - -
86B ALA* 3.5 14.2 + - - +
95B CYS* 1.3 72.0 - - - +
97B PHE* 1.3 62.7 + - - +
98B SER 3.8 3.1 - - - +
99B VAL* 3.7 29.8 - - + -
126B ALA* 4.4 2.0 - - + -
127B ILE 3.7 11.7 - - - +
128B VAL* 4.0 4.0 - - + -
418B GLU 4.4 0.2 + - - -
419B SER 3.9 12.5 - - - +
420B GLN* 5.8 2.8 - - + +
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Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 4.5 5.2 - - - -
95B CYS* 3.4 4.2 + - - -
96B VAL* 1.3 72.4 - - - +
98B SER* 1.3 69.1 + - - +
127B ILE* 2.8 23.3 + - + +
129B PHE* 3.3 39.5 - + + -
170B PRO* 3.3 32.3 - - + -
171B VAL 5.3 0.7 - - - -
172B LEU* 3.8 8.1 - - + -
344B PHE* 3.3 31.9 - + - -
388B GLY 5.7 0.2 - - - -
389B PHE 5.7 0.2 - - - -
393B LYS* 3.3 20.6 - - - -
417B LEU* 3.3 2.3 - - - +
418B GLU* 2.6 62.2 + - + +
647B VAL* 4.9 1.3 - - + -
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.5 1.6 - - - +
97B PHE* 1.3 89.8 - - - +
99B VAL* 1.3 69.5 + - - +
100B GLU* 6.1 1.8 - - - -
125B LEU 4.1 1.8 + - - -
126B ALA* 2.8 25.2 - - - +
127B ILE* 2.9 32.7 + - - +
344B PHE* 4.0 12.0 - - - -
416B LEU 3.4 6.7 - - - -
417B LEU* 3.6 19.7 - - - -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 4.3 4.9 - - + -
68B LEU* 3.5 15.2 - - + +
71B VAL* 3.4 33.0 - - + -
72B MET* 4.7 1.8 - - + +
75B LEU* 4.4 7.9 - - + -
96B VAL* 3.7 14.8 - - + -
98B SER* 1.3 88.3 - - - +
100B GLU* 1.3 64.7 + - - +
124B ALA* 4.1 12.3 - - + -
125B LEU 3.2 6.7 - - - +
126B ALA* 3.4 15.7 - - + -
416B LEU* 3.0 41.8 + - + +
417B LEU* 4.5 1.0 - - - +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ASP* 4.4 1.1 - - + +
63B LEU* 3.2 13.4 - - - +
68B LEU* 4.5 2.2 - - - -
98B SER* 6.2 1.1 - - - -
99B VAL* 1.3 76.7 - - - +
101B LEU* 1.3 74.1 + - - +
124B ALA* 3.3 6.1 - - - -
125B LEU* 3.0 30.9 + - + +
341B LEU 3.8 2.1 - - - +
342B GLY* 3.8 2.8 - - - -
343B ALA* 2.8 46.9 + - + +
344B PHE* 4.1 9.1 + - + -
348B ARG* 3.2 30.0 + - - -
413B TRP* 5.2 3.7 - - + -
417B LEU* 5.2 2.5 - - + -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU 4.5 3.1 - - - +
60B PHE* 4.1 15.0 - - - -
61B ALA 3.8 21.5 - - - +
62B ASP* 4.0 6.0 - - - +
63B LEU* 3.2 32.3 - - + +
100B GLU* 1.3 91.4 + - - +
102B GLN* 1.3 81.8 + - - +
103B LEU* 3.8 25.6 + - + +
104B PRO* 5.2 1.3 - - + -
122B ARG* 3.6 26.5 - - - +
123B GLU 3.6 10.1 - - - +
125B LEU* 4.6 2.3 + - - +
348B ARG* 4.4 14.2 + - - +
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLU 3.4 1.0 + - - -
101B LEU* 1.3 86.9 - - - +
103B LEU* 1.3 92.5 + - - +
104B PRO* 3.6 2.6 - - - +
123B GLU* 3.1 49.5 + - + +
124B ALA* 3.6 11.7 - - - +
125B LEU* 3.6 21.0 - - - +
142B VAL* 4.0 11.0 - - + -
159B ARG* 3.0 30.4 + - - +
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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