Contacts of the strand formed by residues 122 - 132 (chain D) 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 PHE 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D SER 3.8 22.7 - - - -
3D PHE* 3.5 30.4 - + + -
118D VAL* 3.2 5.7 - - - +
119D LYS 3.1 27.2 + - - +
120D ASP 2.8 13.1 + - - +
121D GLN* 1.3 73.7 - - + +
123D TYR* 1.3 70.9 - - - +
124D GLU* 4.7 3.8 - - + -
162D ASP* 3.6 26.7 - - + -
163D LEU* 3.4 21.1 - - - +
164D PHE* 4.1 2.7 - - - -
165D ASP* 2.9 32.1 - - - -
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Residues in contact with TYR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D TYR* 2.8 37.6 + + - -
85D LEU* 3.5 32.1 - - + +
89D LEU* 4.5 4.3 - - + -
116D LEU* 4.4 14.1 - - + -
117D LEU 3.9 3.1 - - - -
118D VAL* 3.4 26.6 - - + +
121D GLN* 3.0 35.9 + - - -
122D PHE* 1.3 83.9 - - - +
124D GLU* 1.3 61.5 + - - +
125D LEU* 4.1 9.0 - - + -
163D LEU* 3.0 15.4 + - + +
164D PHE* 3.0 15.8 - - + -
165D ASP 2.9 22.2 + - - -
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SER* 2.7 30.5 + - - -
3D PHE* 3.3 20.7 + - + +
4D ILE* 2.9 35.8 - - - +
116D LEU* 4.0 1.5 - - - -
117D LEU* 3.0 50.4 + - - +
122D PHE* 4.7 7.6 - - + -
123D TYR* 1.3 74.1 - - - +
125D LEU* 1.3 62.4 + - - +
126D LEU* 3.2 7.6 + - - +
165D ASP* 3.6 7.4 - - + +
167D ASN* 2.9 27.5 + - + +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LEU* 4.6 5.4 - - + -
88D LEU* 3.6 35.7 - - + -
89D LEU* 4.3 12.8 - - + -
112D THR* 4.3 14.6 - - + -
113D ALA* 4.0 13.7 - - + -
115D ILE 4.1 1.6 - - - -
116D LEU* 3.3 29.4 - - + -
123D TYR* 4.1 16.4 - - + -
124D GLU* 1.3 70.7 - - - +
126D LEU* 1.3 59.8 + - - +
127D ASP* 3.8 0.7 + - - +
164D PHE* 4.3 9.6 - - + -
165D ASP 2.7 16.7 + - - +
166D ILE* 3.3 19.9 - - + +
167D ASN 3.0 24.9 + - - +
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Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 4.5 9.9 - - + -
41D VAL* 4.5 3.1 - - + -
45D LEU* 3.6 31.2 - - + -
113D ALA* 4.8 0.7 - - - -
114D ASP* 3.4 7.3 + - - +
115D ILE* 3.0 35.4 + - + +
117D LEU* 3.6 22.4 - - + -
124D GLU* 3.2 6.2 + - + +
125D LEU* 1.3 71.2 - - - +
127D ASP* 1.3 62.7 + - - +
128D VAL* 4.3 16.8 - - + -
167D ASN* 3.4 20.9 - - + +
168D TYR 3.9 15.0 - - - -
169D LEU* 4.0 8.3 - - + +
187D PHE* 4.0 16.6 - - + -
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Residues in contact with ASP 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D THR 4.6 8.4 - - - +
113D ALA* 5.3 0.7 - - - -
114D ASP* 2.9 12.5 - - - +
125D LEU 3.8 1.5 + - - +
126D LEU* 1.3 75.1 - - - +
128D VAL* 1.3 60.8 + - - +
129D LYS* 2.7 16.6 + - - -
143D ILE* 4.7 1.8 - - + +
166D ILE* 5.6 1.8 - - + -
167D ASN 2.8 10.0 + - - +
168D TYR* 3.0 46.0 - - + +
169D LEU 3.1 3.2 + - - -
804D CA 2.2 29.7 - - - -
904D NA 2.1 33.6 - - - -
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Residues in contact with VAL 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE 4.6 1.1 - - - +
38D GLU* 4.3 19.2 - - + +
41D VAL* 3.8 38.4 - - + -
114D ASP* 3.6 10.4 - - + +
115D ILE* 3.8 27.4 - - + -
126D LEU* 4.3 5.4 - - + -
127D ASP* 1.3 76.0 + - - +
129D LYS* 1.3 63.5 + - - +
130D THR* 5.1 3.1 - - + +
169D LEU* 3.4 22.7 - - + +
171D VAL* 4.1 9.9 - - + -
804D CA 2.3 28.6 - - - -
9G A 4.3 3.5 + - - -
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Residues in contact with LYS 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ASP* 2.7 29.3 + - - +
128D VAL* 1.3 74.1 - - - +
130D THR* 1.3 59.4 + - - +
140D PRO* 4.9 15.0 - - + -
141D ASN* 2.7 28.7 + - - +
142D ILE* 3.1 7.9 + - + +
168D TYR* 3.7 22.0 - - + -
169D LEU 3.0 9.3 + - - +
170D GLU* 3.2 9.1 - - + -
171D VAL* 2.7 32.7 + - - +
212D VAL* 4.7 8.1 - - + -
804D CA 4.0 0.4 - - - -
904D NA 2.6 28.3 - - - -
8G G 2.8 12.1 + - - +
9G A 3.6 17.2 + - - +
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Residues in contact with THR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ALA* 4.4 0.6 - - - +
34D GLY* 3.2 38.6 + - - +
37D PHE* 3.6 24.0 - - + -
38D GLU* 4.9 1.8 - - + +
128D VAL* 5.1 3.1 - - + +
129D LYS* 1.3 79.0 - - - +
131D ARG* 1.3 61.7 + - - +
140D PRO* 5.3 5.2 - - - +
171D VAL* 3.6 8.5 - - + -
173D TRP* 3.5 19.4 + - - -
9G A 2.8 45.0 + - - +
10G C 4.0 2.1 + - - -
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Residues in contact with ARG 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D THR* 1.3 76.0 - - - +
132D ASN* 1.3 66.9 + - - +
133D ILE* 3.7 10.9 - - - +
135D LYS 5.1 1.4 + - - -
136D SER* 5.1 5.5 - - - +
137D ALA* 4.3 16.9 + - + +
140D PRO* 6.5 0.9 - - + -
170D GLU* 4.1 9.9 - - + -
171D VAL 3.0 7.9 + - - +
172D ASP* 3.5 23.6 - - - +
173D TRP* 2.7 40.9 + - - -
211D HIS* 3.3 51.4 + - + +
213D ARG* 3.2 43.2 - - - +
214D ASP* 4.5 1.6 + - - -
10G C 3.7 9.4 - - - +
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Residues in contact with ASN 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU* 6.0 1.4 - - - +
131D ARG* 1.3 78.9 - - - +
133D ILE* 1.3 54.9 + - - +
134D SER* 2.9 41.5 + - - -
135D LYS* 2.8 55.9 + - + +
137D ALA* 4.5 2.0 - - - +
173D TRP* 3.4 32.6 + - + -
174D GLU* 4.4 0.8 - - - +
175D LEU 5.1 0.4 - - - +
10G C 3.4 23.1 + - - +
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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