Contacts of the strand formed by residues 122 - 135 (chain A) in PDB entry 2L0W
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 VAL 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ALA* 4.1 4.4 - - + +
35A ARG* 3.3 30.9 + - - +
88A GLY 4.8 4.0 - - - +
89A ALA* 4.4 24.5 - - + -
114A PRO* 3.7 22.4 - - + -
115A VAL 3.5 15.0 - - - +
116A LYS* 3.9 15.1 - - + +
121A ALA* 1.3 70.2 - - - +
123A ILE* 1.3 62.1 + - - +
124A MET 3.6 13.5 - - - +
125A PHE* 3.8 17.7 - - + -
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Residues in contact with ILE 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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33A ASN* 3.8 5.7 + - - -
34A ALA* 2.8 28.9 + - - +
35A ARG* 3.9 26.9 + - + +
115A VAL* 3.1 32.0 + - + +
116A LYS 3.6 4.3 - - - +
117A ASN* 3.5 51.6 - - + +
121A ALA* 4.2 2.9 - - + -
122A VAL* 1.3 78.2 - - - +
124A MET* 1.3 87.9 + - + +
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Residues in contact with MET 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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31A ILE* 4.0 17.9 - - + -
32A ALA 3.4 7.9 - - - +
33A ASN* 4.6 3.4 - - - +
34A ALA* 3.9 2.9 - - - +
42A ILE* 3.8 30.5 - - + -
115A VAL* 2.8 56.4 + - + +
122A VAL* 3.6 5.2 - - - +
123A ILE* 1.3 106.2 - - + +
125A PHE* 1.3 58.9 + - - +
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Residues in contact with PHE 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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30A ILE 3.8 0.3 - - - +
31A ILE* 3.4 4.2 - - - +
32A ALA* 2.8 38.2 + - + +
34A ALA* 3.4 35.9 - - + -
39A CYS* 4.1 9.4 - - + -
85A ALA 4.4 3.6 - - - -
86A LEU* 3.2 49.6 - - + -
88A GLY 3.7 19.1 - - - -
90A GLU 6.0 0.7 - - - -
112A VAL* 3.4 30.5 - - + -
113A VAL 3.8 1.6 - - - -
114A PRO* 4.0 12.3 - - + -
122A VAL* 3.8 18.6 - - + -
124A MET* 1.3 77.0 - - - +
126A ILE* 1.3 61.7 + - - +
127A LEU* 3.9 10.2 + - + +
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Residues in contact with ILE 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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29A PHE* 4.1 16.4 - - + -
30A ILE 3.2 12.1 - - - +
31A ILE* 4.4 20.4 - - + -
111A ASP 3.5 1.6 - - - +
112A VAL* 3.4 2.3 - - - -
113A VAL* 2.7 54.4 + - + +
115A VAL* 3.6 28.3 - - + -
125A PHE* 1.3 73.5 - - - +
127A LEU* 1.3 61.1 + - - +
128A ASN* 3.6 21.3 - - - +
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Residues in contact with LEU 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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29A PHE* 3.2 1.7 - - - -
30A ILE* 2.9 46.2 + - + +
32A ALA* 5.2 0.4 - - + -
64A CYS* 3.4 48.7 - - + +
65A THR 4.7 0.9 - - - +
82A ILE* 4.7 10.8 - - + -
86A LEU* 4.2 5.4 - - + -
110A VAL* 4.0 22.4 - - + -
111A ASP 3.4 2.7 - - - +
112A VAL* 3.7 33.0 - - + -
125A PHE* 3.9 15.3 - - + +
126A ILE* 1.3 72.9 - - - +
128A ASN* 1.3 61.0 + - - +
129A PHE* 4.1 9.6 - - + -
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Residues in contact with ASN 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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27A ARG* 6.1 2.0 - - + -
28A LYS 3.3 11.2 - - - +
29A PHE* 3.3 21.2 - - - +
109A LEU 3.6 0.7 - - - +
110A VAL* 3.4 7.3 - - - +
111A ASP* 2.8 69.9 + - + +
113A VAL* 3.4 16.6 - - - +
126A ILE* 3.6 11.6 + - - +
127A LEU* 1.3 73.4 - - - +
129A PHE* 1.3 65.0 + - - +
130A GLU* 5.7 6.5 - - + +
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Residues in contact with PHE 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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27A ARG* 5.1 0.5 - - - +
28A LYS* 2.9 53.0 + - + +
30A ILE* 3.8 43.5 - - + -
48A PHE* 4.4 9.2 - - + -
51A LEU* 4.5 13.2 - - + -
54A TYR* 4.6 11.4 - - - -
64A CYS 4.6 1.8 - - - -
66A CYS* 4.1 15.9 - - - -
69A LEU* 6.2 0.2 - - + -
98A PHE* 4.2 12.6 - + - -
108A CYS* 3.8 22.2 - - - -
109A LEU 3.5 2.9 - - - -
110A VAL* 3.9 27.8 - - + -
127A LEU* 4.1 13.2 - - + -
128A ASN* 1.3 78.6 - - - +
130A GLU* 1.3 67.0 + - - +
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Residues in contact with GLU 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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27A ARG* 5.4 14.4 - - + +
28A LYS* 5.0 6.1 - - + +
51A LEU* 6.1 0.2 - - - -
93A LYS* 6.1 0.3 - - - +
108A CYS* 3.3 5.5 - - - -
109A LEU* 2.8 60.1 + - + +
111A ASP* 5.7 4.7 - - - +
128A ASN* 5.7 6.6 - - + +
129A PHE* 1.3 80.5 - - - +
131A VAL* 1.3 64.3 + - - +
132A VAL* 3.4 0.7 + - + -
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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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28A LYS* 5.1 8.8 - - - +
51A LEU* 3.6 30.5 - - + -
100A ARG* 4.9 3.8 - - - +
106A PHE* 3.8 29.4 - - + -
107A LEU 3.6 11.0 - - - +
108A CYS* 4.6 0.7 - - - +
130A GLU* 1.3 71.6 - - - +
132A VAL* 1.3 60.9 + - - +
133A MET 4.0 7.9 - - - +
134A GLU* 4.1 16.8 - - + +
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Residues in contact with VAL 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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95A GLU* 3.8 34.1 - - + +
107A LEU* 2.8 31.2 + - + +
109A LEU* 4.6 22.0 - - + +
130A GLU* 3.4 2.0 + - + -
131A VAL* 1.3 74.1 - - - +
133A MET* 1.3 68.4 + - + +
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Residues in contact with MET 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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106A PHE* 3.6 0.2 - - - -
107A LEU* 2.8 40.4 + - + +
131A VAL* 3.6 4.1 - - - +
132A VAL* 1.3 87.7 - - + +
134A GLU* 1.3 72.7 + - - +
135A LYS* 3.6 25.7 + - + -
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Residues in contact with GLU 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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100A ARG* 4.2 21.1 + - - +
104A SER* 6.4 1.1 - - - -
105A CYS 4.1 8.7 - - - +
106A PHE* 3.9 10.7 - - + +
131A VAL* 4.1 12.7 - - + +
133A MET* 1.3 83.4 - - - +
135A LYS* 1.3 68.4 + - - +
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Residues in contact with LYS 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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73A ARG* 6.2 4.7 - - + -
104A SER* 5.4 1.6 - - - -
105A CYS* 3.1 45.8 + - + +
106A PHE* 3.9 1.8 - - - +
107A LEU* 3.8 31.9 - - + +
133A MET* 3.6 18.7 + - + +
134A GLU* 1.3 83.3 - - - +
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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