Contacts of the strand formed by residues 123 - 132 (chain C) in PDB entry 1TW8
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 TYR 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C TYR* 3.6 38.4 + + - -
81C ASN* 3.7 11.7 + - - -
85C LEU* 3.3 37.0 - - + -
89C LEU* 5.3 6.3 - - + -
116C LEU* 5.2 12.8 - - + -
117C LEU 3.7 2.5 - - - +
118C VAL* 3.5 30.5 - - + +
121C GLN* 3.6 26.0 + - - -
122C PHE* 1.3 83.6 - - - +
124C GLU* 1.3 56.4 + - - +
125C LEU* 4.0 11.2 - - + -
163C LEU* 2.7 22.0 + - + -
164C PHE* 3.0 11.8 - - + -
165C ASP* 2.6 35.2 + - - +
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Residues in contact with GLU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER* 3.1 20.3 + - - +
3C PHE* 2.9 39.1 + - + -
4C ILE* 3.8 10.3 + - - +
116C LEU* 3.4 3.2 - - - -
117C LEU* 2.9 57.5 + - + +
122C PHE* 5.2 0.7 - - + -
123C TYR* 1.3 72.7 - - - +
125C LEU* 1.3 64.5 + - - +
126C LEU* 3.4 9.1 + - - +
165C ASP* 3.3 9.0 - - + +
167C ASN* 2.6 34.5 + - + +
187C PHE* 4.6 1.0 - - - -
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU* 5.9 2.5 - - + -
88C LEU* 4.6 17.3 - - + -
89C LEU* 4.1 13.9 - - + -
112C THR* 4.8 14.1 - - + -
113C ALA* 3.9 9.2 - - + -
115C ILE 3.9 2.9 - - - -
116C LEU* 3.4 35.0 - - + -
123C TYR* 4.9 10.8 - - + +
124C GLU* 1.3 71.9 - - - +
126C LEU* 1.3 60.1 + - - +
164C PHE* 4.1 25.1 - - + -
165C ASP 2.7 12.2 + - - +
166C ILE* 2.8 44.0 - - + +
167C ASN 3.0 14.2 + - - -
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Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 5.2 18.4 - - + -
45C LEU* 3.9 27.4 - - + -
113C ALA* 3.8 1.7 - - - +
114C ASP* 2.8 26.2 + - - +
115C ILE* 2.6 39.0 + - + +
116C LEU* 5.3 0.2 - - - -
117C LEU* 5.9 5.8 - - + -
124C GLU* 3.4 8.2 + - + +
125C LEU* 1.3 71.5 - - - +
127C ASP* 1.3 68.3 + - - +
128C VAL* 4.2 12.3 - - + -
167C ASN* 3.9 15.3 - - + +
168C TYR 4.8 0.2 - - - -
169C LEU* 4.0 34.8 - - + +
187C PHE* 5.2 5.8 - - + -
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Residues in contact with ASP 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C THR 4.3 10.0 - - - +
113C ALA* 5.6 0.2 - - - -
114C ASP* 3.3 6.3 - - - +
126C LEU* 1.3 76.8 - - - +
128C VAL* 1.3 61.5 + - - +
129C LYS* 3.1 16.0 + - - +
142C ILE 3.3 0.3 - - - +
143C ILE* 4.1 5.0 - - - +
166C ILE* 4.7 4.3 - - + -
167C ASN 3.2 7.9 + - - +
168C TYR* 3.2 40.4 - - + -
169C LEU 3.1 19.4 + - - -
803C CA 2.2 32.6 - - - -
903C NA 3.3 19.1 - - - -
7H C 5.3 0.5 - - - +
8H G 3.4 3.8 + - - -
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLU* 3.9 42.2 - - + +
41C VAL* 4.7 13.7 - - + -
114C ASP* 2.9 15.4 + - + +
115C ILE* 5.0 1.8 - - + -
126C LEU* 4.5 18.4 - - + -
127C ASP* 1.3 72.3 - - - +
129C LYS* 1.3 61.5 + - - +
130C THR* 4.1 11.9 + - + +
169C LEU* 3.2 15.9 - - + +
171C VAL* 4.0 21.5 - - + -
803C CA 2.4 23.4 - - - -
9H A 3.9 5.9 + - - -
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Residues in contact with LYS 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ASP* 3.1 38.2 + - - +
128C VAL* 1.3 73.0 - - - +
130C THR* 1.3 61.9 + - - +
140C PRO* 4.7 15.9 - - + -
141C ASN 2.5 30.1 + - - -
142C ILE* 2.7 44.4 + - + +
168C TYR* 3.7 6.7 - - + -
169C LEU 2.8 8.8 + - - +
170C GLU* 3.0 13.6 - - + +
171C VAL 2.9 20.3 + - - -
212C VAL* 4.0 25.6 - - + -
803C CA 4.0 0.7 - - - -
903C NA 3.5 2.4 - - - -
8H G 3.9 3.6 + - - -
9H A 3.8 11.4 + - - +
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Residues in contact with THR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ALA 3.6 5.2 + - - -
34C GLY* 3.0 38.9 - - - +
37C PHE* 3.7 18.8 - - + -
38C GLU* 6.0 0.2 - - + -
128C VAL* 4.4 10.8 - - + -
129C LYS* 1.3 74.0 - - - +
131C ARG* 1.3 62.9 + - - +
140C PRO* 5.4 3.6 - - - +
171C VAL* 3.3 19.1 - - + +
173C TRP* 4.2 8.5 - - - -
9H A 2.7 37.3 + - - +
10H C 3.9 8.2 + - - -
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C THR* 1.3 76.4 - - - +
132C ASN* 1.3 74.2 + - - +
133C ILE* 3.5 8.2 + - - +
135C LYS 5.8 2.1 + - - +
136C SER* 6.2 0.8 - - - +
137C ALA* 5.7 9.2 - - + +
138C GLN 5.3 1.3 - - - -
140C PRO* 5.2 6.7 - - + +
170C GLU* 2.6 34.3 + - + +
171C VAL 3.0 7.5 + - - -
172C ASP* 3.5 13.6 - - - +
173C TRP* 2.9 33.7 + - - -
211C HIS* 3.3 41.5 + - - -
213C ARG* 3.2 40.8 - - - +
10H C 3.7 14.4 - - - +
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Residues in contact with ASN 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ARG* 1.3 79.5 + - - +
133C ILE* 1.3 59.7 + - - +
134C SER* 3.0 38.6 + - - +
135C LYS* 3.2 40.6 - - - +
137C ALA* 5.6 0.3 - - - +
173C TRP* 3.6 34.3 - - + +
175C LEU* 5.0 0.7 + - - +
10H C 3.3 29.2 + - - +
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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