Contacts of the strand formed by residues 122 - 128 (chain A) in PDB entry 1UES
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 GLY 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LEU* 4.0 5.6 - - - -
120A GLY 4.0 1.0 + - - -
121A SER* 1.3 78.5 - - - +
123A TRP* 1.3 61.1 + - - -
139A GLU 3.2 12.6 - - - -
141A ASN 3.5 6.5 - - - -
157A ASP* 3.6 0.2 - - - +
158A VAL* 2.8 37.4 + - - +
159A TRP* 3.3 18.0 - - - +
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Residues in contact with TRP 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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70A GLN* 2.9 27.8 + - - -
73A ASN* 3.3 50.1 - - + +
74A HIS* 3.4 31.9 - + - -
77A TYR* 3.9 11.9 - - + -
118A LEU* 3.4 8.6 - - - +
122A GLY* 1.3 73.4 - - - -
124A VAL* 1.3 60.4 + - - +
125A TRP* 3.8 11.4 - - + -
139A GLU* 2.8 38.3 + - + +
141A ASN 3.0 19.6 + - - -
143A GLY 4.0 3.6 - - - -
155A THR* 3.4 25.6 - - + +
156A PHE 3.4 5.4 - - - -
157A ASP* 3.4 46.9 - - + -
158A VAL* 4.4 1.1 - - - -
159A TRP* 3.6 3.4 - - - +
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Residues in contact with VAL 124 (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 PHE* 3.7 33.3 - - + +
114A ALA* 3.8 28.5 - - + +
115A GLY* 4.0 24.7 - - - -
118A LEU* 4.9 1.6 - - + -
123A TRP* 1.3 74.2 - - - +
125A TRP* 1.3 61.6 + - - +
136A ILE* 3.8 7.4 - - + -
137A GLU 3.5 4.9 - - - +
138A LYS* 4.8 1.8 - - + +
155A THR* 2.8 17.5 + - - -
156A PHE* 3.0 47.0 + - + +
158A VAL* 4.7 2.8 - - + +
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Residues in contact with TRP 125 (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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73A ASN* 2.9 33.1 + - - -
76A LEU* 3.5 31.0 - - + -
111A PHE* 3.5 7.3 - - - -
123A TRP* 3.8 11.6 - - + +
124A VAL* 1.3 72.4 - - - +
126A LEU* 1.3 65.8 + - - +
135A SER 3.6 0.3 - - - +
136A ILE* 3.3 5.5 - - - +
137A GLU* 2.8 45.1 + - + +
139A GLU* 3.8 17.5 - - + -
143A GLY 3.9 2.4 + - - -
144A ASN* 3.4 8.5 - - - -
145A PRO* 3.4 35.3 - - + +
152A PRO* 3.2 31.0 - - + -
153A LEU 3.7 2.9 - - - -
154A LEU* 3.2 26.0 - - - -
155A THR* 3.3 39.7 + - + -
190A ARG* 5.0 0.9 - - - -
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Residues in contact with LEU 126 (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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93A LEU* 4.8 3.6 - - + -
97A ILE* 4.7 13.2 - - + -
101A PHE* 4.4 4.5 - - + -
107A PHE* 3.7 35.4 - - + -
111A PHE* 3.5 13.7 - - + -
125A TRP* 1.3 75.2 - - - +
127A ALA* 1.3 60.3 + - - +
134A LEU* 4.2 24.7 - - + -
135A SER 3.5 16.4 - - - +
136A ILE* 4.7 0.7 - - + -
153A LEU* 2.9 48.4 + - + +
154A LEU* 2.8 27.8 + - + +
184A TRP* 4.9 4.7 - - + -
187A VAL* 5.0 0.9 - - + -
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Residues in contact with ALA 127 (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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125A TRP 3.8 0.2 - - - -
126A LEU* 1.3 75.6 - - - +
128A SER* 1.3 62.4 + - - +
133A LYS 3.7 0.2 - - - +
134A LEU* 3.2 7.4 - - - +
135A SER* 2.9 43.6 + - - +
137A GLU* 4.2 7.2 - - + -
145A PRO* 3.9 28.9 - - + -
150A LEU* 4.1 8.5 - - + -
151A ASN 3.1 12.8 - - - +
153A LEU* 4.2 4.3 - - - -
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Residues in contact with SER 128 (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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127A ALA* 1.3 75.8 - - - +
129A ASP* 1.3 68.2 + - - +
132A GLY* 4.4 1.1 - - - -
133A LYS 3.1 9.4 - - - -
134A LEU* 4.0 1.3 - - - -
150A LEU* 3.5 8.2 - - - +
151A ASN* 2.8 56.6 + - - +
153A LEU* 3.8 3.6 - - - +
191A TYR* 3.6 36.6 + - - -
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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