Contacts of the strand formed by residues 138 - 148 (chain A) in PDB entry 1ATH
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 SER 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ARG* 3.7 21.6 + - - -
137A SER* 1.3 79.6 + - - +
139A LYS* 1.3 63.8 + - - +
140A LEU 4.0 0.7 + - - -
221A PHE* 4.2 7.0 - - - -
222A LYS 3.5 4.7 - - - -
223A GLY* 4.5 0.7 - - - -
274A PHE* 5.5 3.1 - - - -
275A LYS 4.6 8.1 + - - -
276A GLY* 6.0 0.2 - - - -
278A ASP* 4.1 11.0 + - - -
279A ILE* 4.0 26.2 - - - -
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Residues in contact with LYS 139 (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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137A SER 4.2 0.6 - - - -
138A SER* 1.3 73.9 - - - +
140A LEU* 1.3 61.9 + - - +
141A VAL* 4.8 16.3 - - + +
195A GLU* 4.1 21.0 + - - -
220A TYR* 3.9 3.4 - - + -
221A PHE* 3.0 31.8 - - - -
222A LYS* 2.9 55.3 + - + +
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Residues in contact with LEU 140 (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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130A LEU* 3.7 44.0 - - + +
131A TYR* 3.9 33.6 - - + +
132A ARG* 4.9 5.6 - - - +
138A SER 4.0 2.7 + - - +
139A LYS* 1.3 71.4 - - - +
141A VAL* 1.3 61.5 + - - +
219A ILE* 4.4 13.9 - - + -
220A TYR 3.1 2.7 - - - +
221A PHE* 3.5 35.7 - - + -
279A ILE* 4.1 11.2 - - + -
421A ILE* 4.1 25.8 - - + -
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 4.8 13.5 - - + +
140A LEU* 1.3 77.6 - - - +
142A SER* 1.3 62.6 + - - +
143A ALA 3.8 1.1 + - - +
193A LYS* 3.5 46.9 - - + +
194A THR* 5.8 0.4 - - + +
195A GLU* 4.6 7.9 - - - +
218A THR 4.6 0.2 - - - -
219A ILE* 3.4 3.3 - - - +
220A TYR* 2.7 63.9 + - + +
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Residues in contact with SER 142 (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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131A TYR* 3.1 45.0 + - - -
140A LEU 4.4 0.2 + - - -
141A VAL* 1.3 74.3 - - - +
143A ALA* 1.3 61.9 + - - +
144A ASN* 3.5 12.5 + - - +
189A TRP* 5.2 0.3 - - - -
193A LYS* 4.2 10.7 - - - +
218A THR 3.6 8.3 - - - -
219A ILE* 4.2 6.5 - - - +
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Residues in contact with ALA 143 (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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141A VAL 3.8 2.6 + - - -
142A SER* 1.3 71.3 - - - +
144A ASN* 1.3 58.0 + - - +
189A TRP* 3.5 26.2 - - + -
190A VAL* 4.5 7.2 - - + -
193A LYS* 3.9 23.6 - - + -
194A THR* 4.8 2.0 - - + -
216A VAL* 5.4 0.4 - - + +
217A ASN* 3.2 3.6 - - - -
218A THR* 2.8 57.6 + - + +
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Residues in contact with ASN 144 (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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82A SER* 3.9 21.6 + - - +
85A THR* 5.0 6.7 - - - +
86A ALA* 3.1 26.5 - - - +
89A MET* 3.4 22.2 - - + +
142A SER* 3.5 14.0 + - - +
143A ALA* 1.3 73.4 + - - +
145A ARG* 1.3 70.9 + - - +
166A TYR 5.7 4.3 - - - +
167A GLY 5.2 0.3 - - - +
168A ALA* 4.1 15.7 - - + +
189A TRP* 3.1 7.6 - - - -
215A LEU* 4.6 1.0 - - - +
216A VAL 3.4 3.6 - - - +
217A ASN* 3.2 23.7 - - - +
218A THR 4.4 2.0 + - - +
219A ILE* 5.9 0.4 - - - +
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Residues in contact with ARG 145 (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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89A MET* 5.0 4.0 - - - -
144A ASN* 1.3 75.7 + - - +
146A LEU* 1.3 62.2 - - - +
147A PHE* 3.4 38.1 - - + -
168A ALA* 5.1 1.9 - - - +
169A LYS* 3.1 63.2 - - - +
171A GLN* 3.3 22.4 + - + +
189A TRP* 3.5 46.3 - - + +
214A VAL 4.2 0.2 - - - +
215A LEU* 3.2 11.2 - - - +
216A VAL 2.8 34.1 + - - -
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Residues in contact with LEU 146 (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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89A MET* 5.0 5.1 - - - -
90A THR* 4.4 11.7 - - + +
145A ARG* 1.3 74.9 - - - +
147A PHE* 1.3 60.2 + - - +
154A PHE* 3.8 17.5 - - + -
158A TYR* 3.2 28.3 - - + +
169A LYS 3.9 2.0 + - - -
170A LEU* 3.4 26.5 - - + +
171A GLN* 2.9 25.8 + - - +
213A LEU* 4.3 28.3 - - + -
214A VAL 3.7 13.7 - - - +
215A LEU* 3.7 26.7 - - + -
354A ILE* 4.9 0.2 - - + -
364A VAL* 5.4 3.8 - - + -
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Residues in contact with PHE 147 (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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145A ARG* 3.4 42.2 - - + -
146A LEU* 1.3 74.6 - - - +
148A GLY* 1.3 58.7 + - - +
154A PHE* 5.1 0.4 - - - -
171A GLN* 3.2 31.6 - - + +
173A LEU* 3.6 19.5 - - + -
175A PHE* 3.6 19.4 - - + -
185A ALA 5.8 0.4 - - - -
186A ILE* 3.6 46.9 - - + -
189A TRP* 3.9 13.7 - + + -
213A LEU* 3.3 6.9 - - - +
214A VAL* 3.0 42.9 + - + -
216A VAL* 4.0 14.6 - - + -
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Residues in contact with GLY 148 (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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146A LEU 4.4 0.2 + - - -
147A PHE* 1.3 75.6 - - - +
149A ASP* 1.3 65.5 + - - +
152A LEU* 4.1 17.5 - - - +
154A PHE* 4.5 7.0 - - - -
171A GLN 3.1 8.2 + - - +
172A PRO* 3.3 15.1 - - - +
173A LEU 3.9 4.1 - - - +
175A PHE* 3.6 6.5 - - - -
212A VAL 3.0 16.6 - - - -
213A LEU* 4.3 3.4 - - - -
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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