Contacts of the strand formed by residues 94 - 102 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLY* 2.8 27.9 + - - +
83A LEU* 3.3 6.8 - - + -
84A VAL* 2.8 28.4 + - - +
93A ASP* 1.3 72.7 - - - +
95A CYS* 1.3 61.3 + - - +
129A PHE 3.3 6.3 - - - +
130A PHE* 3.8 26.7 - - + -
131A GLY 3.2 4.5 + - - -
132A ARG* 2.7 57.7 + - - +
133A GLN* 5.1 2.0 + - - -
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Residues in contact with CYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 4.1 5.2 - - - -
84A VAL 3.2 20.9 - - - +
86A ALA* 3.5 26.7 - - - -
89A ALA* 3.6 19.5 - - + -
93A ASP 5.3 2.2 - - - -
94A ASN* 1.3 74.1 - - - +
96A VAL* 1.3 62.8 + - - +
97A PHE 3.4 2.2 + - - -
128A VAL* 3.1 10.5 - - - +
129A PHE* 3.0 48.7 + - - -
166A TYR* 5.7 0.2 - - - -
172A LEU* 4.3 13.5 - - - -
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A MET* 3.7 22.4 - - + -
75A LEU* 3.8 20.4 - - + -
79A LEU* 4.0 13.0 - - + -
83A LEU* 4.0 10.2 - - + +
84A VAL 4.6 1.6 + - - -
86A ALA* 3.5 14.8 - - - +
95A CYS* 1.3 72.1 - - - +
97A PHE* 1.3 63.8 + - - +
98A SER* 4.0 9.4 - - - +
99A VAL* 3.6 32.1 - - + -
126A ALA* 4.7 0.7 - - + -
127A ILE 3.7 5.4 - - - +
128A VAL* 3.8 18.2 - - + -
416A LEU* 5.9 0.2 - - + -
419A SER 4.2 11.8 + - - +
420A GLN* 6.0 2.8 - - - +
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA* 4.5 6.1 - - + -
95A CYS* 3.4 4.0 + - - -
96A VAL* 1.3 73.6 - - - +
98A SER* 1.3 71.2 + - - +
127A ILE* 2.7 23.3 + - + +
129A PHE* 3.3 32.3 - + + -
170A PRO* 3.8 36.1 - - + -
171A VAL 5.8 0.2 - - - -
172A LEU* 3.3 29.2 - - + -
344A PHE* 4.2 21.5 - + - -
393A LYS* 3.6 16.4 - - - -
417A LEU* 3.8 1.6 - - - +
418A GLU* 2.9 51.6 + - + -
647A VAL* 4.7 2.7 - - + -
648A PHE* 6.0 0.9 - + - -
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A VAL* 3.3 4.3 - - - +
97A PHE* 1.3 89.7 - - - +
99A VAL* 1.3 66.3 + - - +
100A GLU* 4.1 3.8 - - - -
125A LEU 3.8 1.2 + - - +
126A ALA* 3.0 4.0 - - - +
127A ILE* 2.7 58.1 + - - +
344A PHE* 4.1 7.5 - - - -
416A LEU 3.3 7.6 - - - -
417A LEU* 3.3 24.9 - - - -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.0 34.9 - - + +
71A VAL* 3.8 32.1 - - + -
72A MET* 4.4 0.9 - - + +
75A LEU* 3.7 17.7 - - + -
96A VAL* 3.6 22.2 - - + -
98A SER* 1.3 76.5 - - - +
100A GLU* 1.3 61.3 + - - +
124A ALA* 4.5 8.1 - - + -
125A LEU 3.7 2.9 - - - -
126A ALA* 3.8 4.9 - - + -
415A PHE* 5.6 0.3 - - - -
416A LEU* 3.0 37.1 + - + +
417A LEU* 6.0 0.4 - - - +
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.8 6.7 - - - -
68A LEU* 5.0 0.4 - - - -
98A SER* 4.1 4.0 - - - -
99A VAL* 1.3 74.8 - - - +
101A LEU* 1.3 69.6 + - + +
124A ALA* 2.8 9.2 - - - +
125A LEU* 2.6 43.3 + - + +
341A LEU 4.0 2.9 - - - +
342A GLY* 3.3 9.2 - - - -
343A ALA* 3.0 37.8 + - + +
344A PHE* 4.4 10.2 - - + -
348A ARG* 3.2 32.0 + - - +
413A TRP* 5.7 4.0 - - + -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU 4.8 5.8 - - - +
60A PHE 3.7 17.0 - - - +
61A ALA 3.3 27.4 - - - +
62A ASP* 4.3 0.7 - - - -
63A LEU* 3.8 23.9 - - + +
100A GLU* 1.3 87.7 - - + +
102A GLN* 1.3 72.9 + - - +
103A LEU* 3.4 18.3 + - + +
104A PRO* 5.4 1.8 - - + -
122A ARG* 3.7 20.9 - - - +
123A GLU 3.0 26.9 - - - +
125A LEU* 4.2 1.6 - - - +
348A ARG* 4.1 20.8 + - - +
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Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 1.3 81.4 - - - +
103A LEU* 1.3 88.0 + - - +
104A PRO* 3.5 2.8 - - - +
123A GLU* 3.3 36.3 + - + +
124A ALA* 3.5 14.5 - - - +
125A LEU* 3.6 28.2 - - + +
142A VAL* 4.1 6.1 - - + -
159A ARG* 3.1 41.0 + - - +
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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