Contacts of the strand formed by residues 111 - 118 (chain A) in PDB entry 3JTC
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 HIS 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A CYS* 3.5 0.5 - - - -
102A GLU* 2.8 65.8 + - + +
104A PRO* 4.5 5.3 - - + +
109A ARG 3.5 3.4 + - - +
110A ALA* 1.4 73.2 - - - +
112A VAL* 1.3 79.7 + - - +
113A PHE* 4.5 9.8 - + - +
128A PRO* 6.1 2.4 - - + +
129A GLU* 6.1 1.1 - - - -
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Residues in contact with VAL 112 (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 GLY 3.2 8.1 - - - +
101A CYS* 3.8 9.4 - - + -
110A ALA* 3.9 9.3 + - + +
111A HIS* 1.3 94.9 + - - +
113A PHE* 1.3 68.8 + - - +
126A PHE 5.4 0.2 - - - +
128A PRO* 3.6 42.9 - - + +
162A ARG* 5.7 0.2 - - + -
165A LEU* 3.5 52.0 - - + +
166A GLU* 3.9 19.3 - - + +
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Residues in contact with PHE 113 (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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12A HIS* 3.7 30.7 - + - -
98A PHE* 3.5 37.9 - + - -
99A LEU* 3.1 32.6 - - - +
100A GLY* 3.0 44.7 + - - +
102A GLU* 3.9 11.7 - - - -
111A HIS* 4.5 15.9 - + - +
112A VAL* 1.3 83.2 - - - +
114A PHE* 1.3 62.5 + - - +
115A GLU* 4.5 20.4 - - + +
126A PHE* 5.1 7.2 - - - +
127A ARG* 6.3 0.9 - - - +
128A PRO* 5.7 0.7 - - - -
165A LEU* 3.8 8.1 - - - +
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Residues in contact with PHE 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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72A TYR* 3.8 24.9 - + - -
97A CYS* 3.9 15.5 - - + -
98A PHE 3.4 5.2 - - - -
99A LEU* 3.6 36.6 - - + -
113A PHE* 1.3 76.6 - - - +
115A GLU* 1.3 63.3 + - - +
116A VAL* 3.9 19.7 - - + -
125A SER* 3.4 2.5 - - - -
126A PHE* 3.0 42.0 + - + +
133A TRP* 3.5 18.6 - + - -
161A LEU* 4.1 25.1 - - + -
164A PHE* 6.0 0.7 - + - -
165A LEU* 4.2 11.7 - - + -
606A PTY 3.9 20.9 - - + -
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Residues in contact with GLU 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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96A ARG 3.5 1.2 - - - +
97A CYS* 3.3 5.2 - - - +
98A PHE* 2.8 53.9 + - + +
113A PHE* 4.5 18.1 - - + +
114A PHE* 1.3 79.7 - - - +
116A VAL* 1.3 63.9 + - - +
117A ALA 4.2 0.2 - - - -
124A VAL 3.9 3.6 - - - +
125A SER* 3.9 15.9 - - - -
127A ARG* 4.7 9.2 + - - +
136A ASP* 4.8 4.9 - - - +
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Residues in contact with VAL 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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95A ILE* 3.7 26.5 - - + -
96A ARG 3.2 2.9 - - - +
97A CYS* 4.3 3.8 - - - -
114A PHE* 3.9 22.9 - - + -
115A GLU* 1.3 79.0 - - - +
117A ALA* 1.3 65.7 + - - +
118A VAL* 4.7 0.7 - - + -
122A SER* 4.3 0.7 - - - -
123A PHE* 3.0 40.2 + - + +
124A VAL* 2.8 27.0 + - + +
133A TRP* 4.0 18.2 - - + -
136A ASP* 4.7 0.9 - - - +
606A PTY 4.1 20.6 - - + -
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Residues in contact with ALA 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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95A ILE* 3.3 5.7 - - - +
96A ARG* 2.8 48.1 + - + +
116A VAL* 1.3 74.4 - - - +
118A VAL* 1.3 64.8 + - - +
119A ASN 4.2 0.2 - - - -
120A GLY* 4.5 6.7 - - - +
121A SER 3.2 26.5 - - - +
122A SER* 4.2 3.1 - - - +
123A PHE* 4.1 0.4 - - - -
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Residues in contact with VAL 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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93A LEU* 4.7 6.1 - - + -
94A THR 3.4 8.5 - - - +
95A ILE* 4.4 12.1 - - + -
116A VAL* 4.7 0.2 - - + -
117A ALA* 1.3 77.0 - - - +
119A ASN* 1.3 82.0 + - + +
120A GLY 3.2 0.9 - - - -
121A SER* 2.8 23.2 + - - +
123A PHE* 3.6 38.3 - - + +
604A NAG 4.3 19.7 - - + +
606A PTY 3.9 26.5 - - + -
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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