Contacts of the strand formed by residues 127 - 133 (chain B) in PDB entry 3CIT
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 GLY 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B LEU 3.0 15.0 - - - -
67B GLU* 4.0 1.3 - - - -
68B TRP* 3.4 15.4 - - - -
117B PRO* 3.7 0.5 - - - +
118B LEU* 2.8 33.2 + - - -
125B SER* 3.6 8.7 + - - -
126B PHE* 1.3 81.0 - - - +
128B THR* 1.3 65.0 + - - -
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Residues in contact with THR 128 (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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64B LEU 3.9 0.3 - - - +
65B LEU* 3.7 5.9 - - - -
66B LEU* 2.8 43.8 + - + +
68B TRP* 4.0 20.6 - - + -
93B ALA* 5.0 5.6 - - - +
94B ASP 5.7 0.4 - - - +
115B LEU* 4.2 11.6 - - + +
116B LEU 3.3 19.5 + - - -
117B PRO* 3.7 6.1 - - - +
118B LEU* 4.0 3.2 - - - +
127B GLY* 1.3 75.7 - - - -
129B LEU* 1.3 70.8 + - - +
130B VAL* 3.8 17.9 + - + +
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Residues in contact with LEU 129 (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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50B VAL* 5.0 5.4 - - + -
51B LEU* 3.7 36.6 - - + +
54B ALA* 4.8 14.1 - - + -
64B LEU 3.6 1.6 - - - +
65B LEU* 3.9 20.0 - - + -
114B LEU 3.6 1.1 - - - +
115B LEU* 3.5 2.6 - - - -
116B LEU* 2.9 60.0 + - + +
118B LEU* 4.3 3.9 - - + +
128B THR* 1.3 75.0 + - - +
130B VAL* 1.3 59.3 + - - +
131B LEU* 4.1 5.2 - - + -
148B LEU* 5.5 1.8 - - + +
151B LEU* 5.9 2.2 - - + -
152B ALA* 4.5 18.2 - - + +
155B LEU* 4.0 26.9 - - + -
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Residues in contact with VAL 130 (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 GLY* 3.0 5.4 - - - -
64B LEU* 2.8 53.9 + - + +
66B LEU* 4.0 17.5 - - + -
86B LEU* 5.7 0.4 - - + -
89B LEU* 4.0 21.8 - - + -
113B VAL* 3.7 25.1 - - + -
114B LEU 3.5 2.7 - - - -
115B LEU* 4.0 11.7 - - + -
128B THR* 3.9 22.9 - - + +
129B LEU* 1.3 78.6 - - - +
131B LEU* 1.3 66.7 + - - +
132B ALA* 4.8 1.8 - - + -
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Residues in contact with LEU 131 (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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51B LEU* 3.9 21.1 - - + -
54B ALA* 3.9 24.7 - - + +
55B CYS* 3.9 11.9 - - - +
58B VAL* 3.7 25.6 - - + -
60B MSE 3.4 17.9 - - + +
62B HIS 3.7 4.3 - - - +
113B VAL* 3.3 3.5 - - - +
114B LEU* 2.8 59.0 + - + +
116B LEU* 4.4 9.9 - - + -
129B LEU* 4.8 6.3 - - + -
130B VAL* 1.3 82.8 - - - +
132B ALA* 1.3 61.5 + - - +
148B LEU* 4.4 7.9 - - + -
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Residues in contact with ALA 132 (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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60B MSE 3.6 4.8 - - - +
61B ASP 3.4 4.7 + - - -
62B HIS* 2.8 44.2 + - + +
86B LEU* 4.6 2.7 - - + -
89B LEU* 4.5 8.7 - - + -
110B LEU* 4.0 23.3 - - + -
112B CYS 3.3 9.4 - - - +
113B VAL* 3.9 15.3 - - + -
130B VAL* 4.1 2.2 - - + -
131B LEU* 1.3 75.7 - - - +
133B ASN* 1.3 60.8 + - - +
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Residues in contact with ASN 133 (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 ALA 4.2 0.6 + - - -
60B MSE 3.2 20.6 - - + -
61B ASP* 3.0 17.5 + - - +
110B LEU* 3.3 8.0 - - - -
111B PRO* 3.1 25.5 - - - +
112B CYS* 2.9 11.7 + - + +
132B ALA* 1.3 73.4 - - - +
134B SER* 1.3 58.9 + - - +
135B VAL 2.8 32.1 + - - +
137B ILE* 3.5 18.4 - - + +
176B GOL 2.7 46.5 + - - -
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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