Contacts of the strand formed by residues 119 - 123 (chain A) in PDB entry 4TZ1
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 THR 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A VAL* 4.1 12.9 - - + +
86A PHE* 6.1 0.2 - - - -
89A GLN* 3.8 16.1 - - - +
99A TYR* 3.3 7.6 - - + +
101A LEU* 3.8 32.1 - - + -
114A GLN 5.9 0.2 - - - +
115A ILE* 3.4 19.3 - - + +
116A GLY 3.7 14.9 + - - +
117A PHE 3.0 13.2 + - - -
118A TYR* 1.3 76.6 + - - +
120A SER* 1.3 64.8 + - - +
153A TRP 3.9 1.6 + - - -
154A ARG* 3.3 9.3 - - - +
155A SER 3.3 18.2 + - - -
356A LEU* 4.6 1.6 - - - -
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Residues in contact with SER 120 (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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99A TYR 3.0 5.5 + - - -
100A ALA* 3.3 14.9 - - - +
101A LEU* 2.8 31.5 + - - +
102A MET* 5.5 3.6 - - - +
118A TYR 4.2 0.2 - - - -
119A THR* 1.3 75.3 - - - +
121A ILE* 1.3 61.7 + - - +
122A ALA* 6.1 0.9 - - - -
155A SER* 3.2 24.0 - - - -
354A LEU* 4.7 0.9 - - - -
355A GLY* 3.1 29.5 + - - -
356A LEU* 4.7 3.4 - - - -
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Residues in contact with ILE 121 (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* 3.2 11.7 - - + +
103A PHE* 3.5 33.7 - - + -
113A ALA* 4.0 27.1 - - + -
115A ILE* 4.1 17.5 - - + -
120A SER* 1.3 76.3 - - - +
122A ALA* 1.3 65.8 - - - +
133A PHE* 4.0 13.2 - - + -
137A VAL* 3.6 27.4 - - + -
155A SER* 2.9 18.5 + - - +
156A ALA* 3.3 7.4 - - + -
157A GLU* 3.0 21.7 + - - +
159A LEU* 4.2 7.9 - - + -
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Residues in contact with ALA 122 (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 2.9 6.7 + - - +
102A MET* 3.4 27.2 - - + -
103A PHE* 2.9 27.3 + - - -
120A SER* 6.1 1.3 - - - -
121A ILE* 1.3 79.3 - - - +
123A GLY* 1.3 65.6 + - - +
157A GLU* 3.0 28.5 - - + +
158A ASN* 5.0 0.2 - - + -
159A LEU* 3.9 8.7 - - - -
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Residues in contact with GLY 123 (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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103A PHE 3.5 7.4 - - - -
122A ALA* 1.3 82.0 - - - +
124A LEU* 1.3 63.8 + - - +
125A GLY 3.6 2.5 - - - -
131A THR* 3.8 4.5 - - - -
157A GLU 3.1 9.5 + - - -
158A ASN* 3.0 34.6 + - - +
159A LEU* 3.5 12.7 - - - +
268A PHE* 5.2 0.2 - - - -
269A LEU 4.0 7.4 - - - +
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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