Contacts of the strand formed by residues 127 - 133 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LEU 2.9 15.0 - - - -
67A GLU* 4.0 1.6 - - - -
68A TRP* 3.4 13.0 - - - -
117A PRO* 3.6 1.2 - - - +
118A LEU* 2.8 35.8 + - - -
125A SER* 2.9 9.9 + - - -
126A PHE* 1.3 80.3 - - - +
128A THR* 1.3 62.4 + - - -
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Residues in contact with THR 128 (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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65A LEU* 3.5 3.0 - - - +
66A LEU* 3.0 33.1 + - - +
68A TRP* 3.1 24.3 - - - -
94A ASP* 4.6 8.1 - - - +
115A LEU* 3.9 22.0 - - + -
116A LEU 3.5 25.6 - - - +
117A PRO* 4.0 4.9 - - + +
118A LEU* 3.9 4.6 - - - +
127A GLY* 1.3 70.8 + - - -
129A LEU* 1.3 71.7 + - - +
130A VAL* 3.7 10.9 + - - +
178A GOL 4.4 9.0 + - - +
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Residues in contact with LEU 129 (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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47A ARG 5.8 0.4 - - - +
50A VAL* 4.0 23.3 - - + -
51A LEU* 3.5 40.2 - - + +
54A ALA* 4.1 14.8 - - + -
64A LEU 3.8 4.3 - - - +
65A LEU* 3.9 14.8 - - + -
114A LEU 3.5 1.7 - - - +
115A LEU* 3.5 3.5 - - - -
116A LEU* 2.8 63.6 + - + +
118A LEU* 3.5 11.3 - - + +
128A THR* 1.3 71.3 - - - +
130A VAL* 1.3 59.1 + - - +
131A LEU* 4.0 9.2 - - + -
148A LEU 4.8 2.9 - - - +
151A LEU* 5.7 0.7 - - + -
152A ALA* 4.3 13.2 - - + -
155A LEU* 5.3 1.8 - - + -
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Residues in contact with VAL 130 (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 GLY* 3.0 5.0 - - - -
64A LEU* 2.8 62.4 + - + +
66A LEU* 4.2 5.8 - - + -
89A LEU* 3.9 25.6 - - + -
113A VAL* 3.6 28.5 - - + -
114A LEU 3.5 2.9 - - - -
115A LEU* 3.8 16.6 - - + -
128A THR* 3.9 15.9 - - - +
129A LEU* 1.3 76.2 - - - +
131A LEU* 1.3 64.6 + - - +
178A GOL 4.1 12.1 - - - +
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Residues in contact with LEU 131 (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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51A LEU* 4.0 11.4 - - + -
54A ALA* 4.0 17.5 - - + +
55A CYS* 3.9 20.2 - - - -
58A VAL* 3.9 15.3 - - + -
60A MSE 3.7 17.3 - - + -
62A HIS 3.7 4.9 - - - +
113A VAL* 3.2 5.5 - - - +
114A LEU* 2.8 49.0 + - + +
116A LEU* 4.3 9.2 - - + -
129A LEU* 4.1 12.6 - - + -
130A VAL* 1.3 80.9 - - - +
132A ALA* 1.3 62.2 + - - +
148A LEU* 3.6 30.3 - - + -
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Residues in contact with ALA 132 (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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60A MSE 3.6 6.9 - - - +
61A ASP 3.4 4.3 + - - -
62A HIS* 2.9 38.4 + - + +
63A GLY* 5.2 0.7 - - - +
89A LEU* 4.5 9.4 - - + -
110A LEU* 3.9 29.2 - - + -
112A CYS 3.2 11.9 - - - +
113A VAL* 4.0 11.0 - - + -
130A VAL* 5.1 0.2 - - + -
131A LEU* 1.3 77.1 - - - +
133A ASN* 1.3 61.2 + - - +
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Residues in contact with ASN 133 (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 ALA 4.3 0.2 - - - -
60A MSE 3.4 17.8 - - + -
61A ASP* 3.0 13.3 + - - +
110A LEU* 3.3 11.2 - - - -
111A PRO* 3.2 23.0 - - - +
112A CYS* 2.9 14.2 + - + +
132A ALA* 1.3 74.7 - - - +
134A SER* 1.3 60.0 + - - +
135A VAL* 2.8 33.8 + - - +
137A ILE* 3.5 17.6 - - + +
176A GOL 2.7 50.6 + - - -
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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