Contacts of the strand formed by residues 193 - 201 (chain A) in PDB entry 4TZQ
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 PHE 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ASN 5.3 1.8 - - - -
59A ILE* 4.4 24.7 - - + -
112A ILE* 3.8 23.6 - - + -
113A THR 3.3 15.9 - - - +
114A ASN 3.8 6.7 + - - -
189A LEU* 4.2 27.6 - - + -
190A PRO* 3.3 33.9 - - + -
191A GLU 4.9 0.2 - - - -
192A GLU* 1.3 73.8 - - - +
194A THR* 1.3 71.5 + - - +
195A ALA* 4.4 13.7 - - + -
496B ILE* 4.8 5.2 - - + -
497B ASN* 3.8 3.2 + - - -
498B ARG* 3.1 62.8 + - + +
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Residues in contact with THR 194 (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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111A VAL 3.5 1.6 - - - +
112A ILE* 3.4 1.0 - - - -
113A THR* 2.8 40.4 + - - +
114A ASN 4.3 0.5 + - - -
115A ASN* 3.9 2.2 - - - -
116A GLU* 3.3 48.2 + - + +
117A GLY 5.0 0.7 - - - +
193A PHE* 1.3 74.5 + - - +
195A ALA* 1.3 67.8 + - - +
196A ASN* 5.1 6.0 - - + +
198A ARG* 6.4 0.2 - - - +
495B SER* 4.7 8.3 - - - -
496B ILE 3.5 4.9 - - - +
497B ASN* 3.3 31.0 + - - +
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Residues in contact with ALA 195 (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 ILE* 4.5 8.7 - - + -
110A LEU* 4.3 13.9 - - + -
111A VAL 3.3 7.4 - - - +
112A ILE* 4.2 16.8 - - + -
193A PHE* 4.3 11.6 - - + -
194A THR* 1.3 75.0 - - - +
196A ASN* 1.3 59.2 + - - +
495B SER* 3.4 4.0 - - - -
496B ILE* 2.7 56.6 + - + +
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Residues in contact with ASN 196 (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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110A LEU* 3.4 9.7 - - - +
111A VAL 2.6 42.7 + - - +
117A GLY* 5.7 4.0 - - - +
194A THR* 5.5 5.4 - - + +
195A ALA* 1.3 75.8 - - - +
197A PHE* 1.3 60.6 + - - +
198A ARG* 3.0 40.0 + - - +
491B VAL* 3.7 21.6 - - - +
492B SER* 3.7 13.1 + - - +
494B THR 3.9 9.0 - - - +
495B SER* 4.0 9.3 - - - +
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Residues in contact with PHE 197 (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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50A PHE* 3.6 32.1 - + + -
54A LEU* 4.4 11.4 - - + -
89A ILE* 3.9 22.4 - - + -
92A LEU* 4.1 13.2 - - + -
93A LEU* 3.5 33.4 - - + -
108A VAL* 4.4 8.7 - - + -
109A SER 3.2 16.8 - - - +
110A LEU* 3.6 24.0 - - + -
196A ASN* 1.3 76.5 - - - +
198A ARG* 1.3 62.8 + - - +
214A PHE* 3.5 20.9 - - + -
491B VAL* 4.4 0.5 - - - +
492B SER* 2.9 39.8 + - - -
494B THR* 5.8 1.1 - - + -
496B ILE* 5.8 2.7 - - + -
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Residues in contact with ARG 198 (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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108A VAL* 4.8 0.4 - - - -
109A SER* 2.9 31.0 + - - +
111A VAL* 3.6 26.8 + - + +
113A THR* 3.7 19.2 + - - +
117A GLY* 4.5 7.2 + - - +
118A ASP 3.0 33.5 + - - +
119A LEU* 4.0 5.1 + - - +
194A THR* 6.4 0.2 - - - +
196A ASN* 3.0 36.6 + - - +
197A PHE* 1.3 79.5 - - - +
199A LEU* 1.3 61.4 + - - +
214A PHE* 4.8 0.4 - - - -
220A PHE* 3.0 52.6 + - + -
221A TYR* 3.9 9.9 - - - +
490B GLY 3.4 7.0 - - - +
491B VAL* 4.5 14.3 - - + +
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Residues in contact with LEU 199 (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 ALA* 4.6 7.0 - - + -
105A LEU* 4.3 3.1 - - + -
107A GLU 3.1 14.6 - - - +
108A VAL* 4.2 6.7 - - + -
198A ARG* 1.3 75.0 - - - +
200A GLU* 1.3 66.5 + - - +
201A TYR* 3.7 38.4 - - + +
211A ILE* 3.6 25.8 - - + -
214A PHE* 3.4 41.3 - - + -
220A PHE* 3.4 8.7 - - - -
489B TYR* 3.3 8.8 - - - +
490B GLY* 2.8 42.4 + - - +
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Residues in contact with GLU 200 (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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105A LEU* 3.9 5.0 - - - +
106A LYS* 2.9 53.1 + - + +
107A GLU* 3.0 19.9 + - + +
199A LEU* 1.3 77.7 - - - +
201A TYR* 1.3 72.0 + - - +
220A PHE* 4.0 17.1 - - + -
487B ALA 4.1 9.4 + - - -
488B ARG 3.4 14.6 - - - +
489B TYR* 3.4 30.9 + - + -
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Residues in contact with TYR 201 (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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104A PHE 3.4 18.4 - - - +
106A LYS* 3.8 11.0 + - - +
199A LEU* 3.7 19.1 - - + +
200A GLU* 1.3 86.8 - - - +
202A THR* 1.3 70.1 + - - +
205A ALA* 3.9 4.7 - - + -
209A PHE* 3.9 18.6 - + - -
210A ARG* 3.6 9.9 - - - +
211A ILE* 3.1 48.1 + - + +
214A PHE* 4.6 4.7 + - - +
216A ASP* 4.1 3.4 + - - -
488B ARG* 3.2 70.7 + - + +
489B TYR 4.0 14.8 - - - -
490B GLY* 4.2 1.0 - - - -
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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