Contacts of the strand formed by residues 126 - 138 (chain A) in PDB entry 3S3J
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 GLN 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA 4.1 15.1 - - - +
3A GLU* 5.6 0.2 - - - -
4A GLU* 3.5 35.6 + - + +
122A SER* 3.8 1.0 - - - -
123A THR* 3.2 35.6 + - - +
125A TYR* 1.3 78.4 - - + +
127A GLY* 1.3 57.7 + - - +
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Residues in contact with GLY 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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4A GLU* 3.2 10.0 - - - +
120A GLU* 6.4 0.9 - - - -
121A ALA 3.7 6.7 - - - -
122A SER* 4.2 8.5 - - - -
125A TYR 3.7 2.5 + - - -
126A GLN* 1.3 75.0 - - - +
128A SER* 1.3 62.7 + - - -
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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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4A GLU* 3.0 25.2 + - - -
5A LEU 5.6 1.5 + - - -
119A LEU 4.6 0.2 - - - -
120A GLU* 3.5 9.7 - - - +
121A ALA* 3.0 33.7 + - - -
127A GLY* 1.3 72.2 + - - -
129A SER* 1.3 63.4 + - - +
130A PHE* 4.2 23.1 - - - -
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Residues in contact with SER 129 (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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118A SER* 6.4 0.9 - - - -
119A LEU 3.4 7.7 + - - -
120A GLU* 4.5 13.0 + - - +
128A SER* 1.3 77.3 + - - +
130A PHE* 1.3 72.0 + - - +
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Residues in contact with PHE 130 (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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5A LEU 4.8 8.1 - - - -
6A VAL* 5.6 0.4 - - - -
7A LEU* 3.9 58.1 - - + -
118A SER* 3.3 6.6 - - - -
119A LEU* 2.8 49.1 + - + +
121A ALA* 4.3 18.2 - - + -
128A SER* 4.2 24.7 - - - -
129A SER* 1.3 79.4 - - - +
131A VAL* 1.3 68.0 + - - +
132A LEU* 3.6 4.0 - - + -
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Residues in contact with VAL 131 (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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116A ARG* 4.0 28.3 - - + +
117A LEU 3.8 8.3 - - - +
118A SER* 4.0 11.0 - - - +
130A PHE* 1.3 77.3 - - - +
132A LEU* 1.3 62.8 + - - +
133A GLY* 4.0 13.9 - - - +
134A HIS* 4.9 6.1 - - + +
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Residues in contact with LEU 132 (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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7A LEU* 3.6 31.9 - - + -
10A CYS* 4.0 41.2 - - + +
12A LEU* 5.2 5.4 - - + +
41A LEU* 4.6 1.8 - - + -
43A LEU* 4.2 8.7 - - + -
59A PHE* 3.5 33.4 - - + -
117A LEU* 2.9 28.9 + - + +
119A LEU* 3.8 25.6 - - + +
130A PHE* 3.6 3.3 + - + -
131A VAL* 1.3 75.9 - - - +
133A GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 133 (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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12A LEU* 5.5 9.0 - - - -
116A ARG* 3.6 5.4 - - - +
117A LEU* 2.7 37.6 + - - +
131A VAL* 3.4 6.6 - - - -
132A LEU* 1.3 83.3 - - - +
134A HIS* 1.3 68.1 + - - -
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Residues in contact with HIS 134 (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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12A LEU* 4.1 20.8 - - - +
30A LYS* 5.3 6.1 - - + +
31A LEU* 4.1 6.9 + - - +
114A LEU* 3.9 25.7 - - + +
115A TYR 3.1 17.2 + - - +
116A ARG* 3.6 33.1 - - + +
117A LEU* 5.7 0.2 - - - -
131A VAL* 4.9 5.5 - - + +
133A GLY* 1.3 81.0 - - - -
135A PHE* 1.3 65.2 + - - +
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Residues in contact with PHE 135 (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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30A LYS* 6.2 0.2 - - - -
31A LEU* 3.1 32.1 - - + +
33A VAL* 3.9 18.2 - - + -
39A PHE* 4.4 19.1 - + - -
61A VAL* 4.2 7.9 - - + -
88A TRP* 4.0 21.3 - + - -
104A LEU* 6.0 0.4 - - + -
113A GLY 3.9 0.2 - - - +
114A LEU* 3.6 2.3 - - - +
115A TYR* 2.7 73.8 + + + +
117A LEU* 4.2 28.9 - - + -
134A HIS* 1.3 77.2 - - - +
136A ILE* 1.3 66.5 + - - +
137A LEU* 4.0 17.7 - - + -
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Residues in contact with ILE 136 (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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30A LYS* 5.7 8.5 - - + -
31A LEU 2.8 12.9 + - - +
32A VAL* 3.4 11.6 - - + +
33A VAL* 2.8 30.8 + - - +
113A GLY* 3.5 12.3 - - - +
114A LEU* 3.9 20.6 - - + -
135A PHE* 1.3 77.7 - - - +
137A LEU* 1.3 62.5 + - - +
138A LEU* 3.9 16.4 - - + -
190A LEU* 3.8 30.3 - - + -
191A ASP* 4.3 11.0 - - - +
194A LEU* 3.7 26.9 - - + -
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Residues in contact with LEU 137 (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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33A VAL* 3.4 17.3 - - + -
34A ARG 3.8 7.0 - - - +
35A ARG* 3.7 34.3 - - + +
88A TRP* 4.3 11.9 - - + -
106A THR* 4.1 13.7 - - + +
110A ALA* 4.0 21.3 - - + +
111A PRO 3.8 10.1 - - - +
112A ILE* 3.0 8.9 - - - +
113A GLY 2.9 29.3 + - - +
115A TYR* 3.7 35.4 - - + +
135A PHE* 4.0 4.7 - - + -
136A ILE* 1.3 75.0 - - - +
138A LEU* 1.3 64.5 + - - +
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Residues in contact with LEU 138 (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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23A THR* 4.7 0.9 - - + -
26A LEU* 3.9 13.9 - - + -
32A VAL* 3.7 28.3 - - + -
33A VAL 2.9 11.2 + - - +
34A ARG* 3.5 16.8 - - + +
35A ARG* 3.0 25.8 + - - +
112A ILE* 3.8 9.6 - - + -
113A GLY 5.5 0.7 - - - +
136A ILE* 3.9 17.0 - - + -
137A LEU* 1.3 82.0 - - - +
139A PHE* 1.3 71.0 + - - +
190A LEU* 4.1 14.1 - - + -
194A LEU* 5.7 0.9 - - + -
290A CYS 3.4 20.6 - - - +
291A LEU* 3.5 22.4 - - + +
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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