Contacts of the strand formed by residues 112 - 118 (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 CYS 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A MSE 4.2 1.8 - - - -
102A TRP* 3.7 24.7 - - + -
103A LEU 3.4 5.4 - - - -
104A GLU* 5.2 6.5 - - - -
110A LEU 3.1 0.5 + - - +
111A PRO* 1.3 84.3 - - - +
113A VAL* 1.3 63.8 + - - +
132A ALA* 3.2 4.2 - - - +
133A ASN* 2.9 33.2 + - + +
135A VAL 4.4 4.5 - - - +
136A ALA* 3.6 11.7 - - - -
137A ILE* 3.4 45.5 - - + -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MSE 4.3 0.2 - - - -
89A LEU* 3.9 20.9 - - + -
101A GLN 3.7 0.9 - - - +
102A TRP* 3.5 8.8 - - - -
103A LEU* 2.7 55.1 + - + +
105A ARG* 4.1 10.8 - - - -
110A LEU 3.9 14.1 - - - +
112A CYS* 1.3 80.5 - - - +
114A LEU* 1.3 62.8 + - - +
115A LEU* 3.7 16.2 - - + -
130A VAL* 3.6 22.4 - - + -
131A LEU 3.2 10.5 - - - +
132A ALA* 4.0 6.7 - - + -
178A GOL 4.3 4.0 - - - +
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Residues in contact with LEU 114 (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 4.2 3.1 - - + +
100A PRO* 4.3 2.7 - - + -
101A GLN 3.4 17.9 - - - +
102A TRP* 3.8 23.6 - - + +
113A VAL* 1.3 74.0 - - - +
115A LEU* 1.3 67.5 + - - +
116A LEU* 4.1 21.5 - - + +
129A LEU 3.5 1.6 - - - +
130A VAL* 3.5 4.7 - - - -
131A LEU* 2.8 65.1 + - + +
140A PRO* 4.8 10.5 - - + -
145A ILE* 4.3 32.5 - - + -
148A LEU* 4.1 15.5 - - + -
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Residues in contact with LEU 115 (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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94A ASP* 4.6 11.2 - - - +
100A PRO* 3.1 29.6 - - - +
101A GLN* 2.9 46.5 + - + +
103A LEU* 4.3 7.0 - - + -
113A VAL* 3.7 23.8 - - + -
114A LEU* 1.3 73.0 - - - +
116A LEU* 1.3 60.5 + - - +
117A PRO* 4.0 2.2 - - + +
128A THR* 3.9 10.5 - - + -
129A LEU 3.5 1.8 - - - -
130A VAL* 3.8 25.6 - - + -
178A GOL 3.8 33.0 - - - +
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Residues in contact with LEU 116 (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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100A PRO* 3.8 17.5 - - + -
114A LEU* 4.1 25.4 - - + +
115A LEU* 1.3 81.5 - - - +
117A PRO* 1.3 69.9 - - - +
118A LEU* 3.7 3.3 - - - +
128A THR* 3.6 2.9 - - - +
129A LEU* 2.8 60.5 + - + +
131A LEU* 4.3 11.2 - - + -
145A ILE* 4.3 5.4 - - + +
148A LEU* 3.6 26.7 - - + +
149A GLN* 4.0 22.4 - - + +
152A ALA* 4.0 14.1 - - + -
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Residues in contact with PRO 117 (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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97A ALA* 3.9 30.3 - - + +
99A GLY 3.3 31.2 - - - +
115A LEU* 4.0 3.1 - - + +
116A LEU* 1.3 86.2 - - - +
118A LEU* 1.3 61.6 + - - +
119A ARG* 4.0 4.6 + - + +
125A SER* 3.7 13.2 - - - +
127A GLY 3.6 6.1 - - - +
128A THR* 4.0 6.9 - - + +
149A GLN* 2.9 40.4 - - - +
152A ALA* 3.8 7.1 - - - +
153A THR* 4.8 1.4 + - - -
39B ILE* 6.1 0.9 - - - +
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Residues in contact with LEU 118 (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* 3.8 21.3 - - + -
67A GLU* 4.9 4.9 - - + -
116A LEU 3.7 3.6 - - - +
117A PRO* 1.3 72.9 - - - +
119A ARG* 1.3 61.2 + - - +
125A SER* 2.9 19.6 + - - -
126A PHE* 3.0 30.7 + - + -
127A GLY* 2.8 18.7 + - - +
128A THR* 3.9 3.4 - - - +
129A LEU* 3.5 27.6 - - + +
152A ALA* 3.8 23.1 - - + +
155A LEU* 4.2 6.1 - - + -
156A ALA* 3.7 15.0 - - + -
159A LEU* 3.8 28.9 - - + -
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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