Contacts of the strand formed by residues 119 - 127 (chain A) in PDB entry 3SBW
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ARG* 4.5 8.3 - - - -
117A ASP 3.3 3.2 + - - -
118A SER* 1.3 74.8 - - - +
120A ILE* 1.3 66.7 + - - -
121A TYR* 3.7 13.5 - - - -
141A GLU* 3.4 5.6 + - - +
142A LEU 2.9 32.5 + - - +
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Residues in contact with ILE 120 (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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69A ARG* 3.7 4.9 - - - +
70A LEU* 2.8 54.0 + - + +
119A GLY* 1.3 73.5 - - - -
121A TYR* 1.3 66.3 + - - +
139A GLY* 4.3 2.5 - - - -
140A ALA 3.5 7.0 - - - +
141A GLU* 3.5 42.8 - - + +
93B ALA* 3.8 34.5 - - + +
94B ARG 4.3 0.4 - - - +
96B GLN* 4.4 15.7 - - + +
111B LEU* 3.8 22.0 - - + -
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Residues in contact with TYR 121 (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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37A PHE* 3.8 9.0 - - + -
52A PHE* 4.6 7.0 - + + -
67A TRP* 3.3 28.5 - + - +
68A ASN 3.1 15.9 - - - +
69A ARG* 3.6 35.7 + - + -
70A LEU* 4.7 1.1 - - - +
79A GLN* 4.0 11.9 - - + -
95A PHE* 4.1 17.5 - + - -
110A ILE* 4.2 8.2 - - + +
117A ASP* 2.5 34.8 + - - -
119A GLY 3.7 19.3 - - - -
120A ILE* 1.3 79.4 - - - +
122A LEU* 1.3 63.1 + - - +
139A GLY* 3.2 6.1 - - - -
140A ALA* 2.8 38.5 + - - +
142A LEU* 4.1 16.2 - - + -
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Residues in contact with LEU 122 (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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37A PHE* 3.8 9.4 - - - -
67A TRP* 3.6 2.9 - - - -
68A ASN* 2.8 51.2 + - + +
70A LEU* 4.2 26.0 - - + +
76A THR* 6.2 0.4 - - + -
121A TYR* 1.3 77.1 - - - +
123A CYS* 1.3 73.4 + - - +
124A GLY* 5.1 0.2 - - - -
136A GLU* 3.9 23.8 - - + +
137A SER* 3.4 13.7 - - - +
138A PRO 3.7 4.0 - - - +
139A GLY 4.7 2.0 - - - +
94B ARG* 4.4 5.4 - - - -
112B ASP* 3.6 16.2 - - - +
114B ARG* 3.5 28.0 - - - +
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Residues in contact with CYS 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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35A LEU* 3.6 8.6 - - - +
36A THR 4.2 0.9 - - - -
37A PHE* 3.6 17.1 - - + -
54A CYS* 2.1 54.3 - - + -
65A LEU* 4.8 1.1 - - + -
66A ASN 3.2 8.5 - - - +
67A TRP* 4.5 0.7 - - - +
108A MET* 4.0 11.4 - - + -
122A LEU* 1.3 79.5 - - - +
124A GLY* 1.3 58.7 + - - +
136A GLU* 3.6 1.2 - - - -
137A SER* 2.9 44.9 + - - -
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Residues in contact with GLY 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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35A LEU* 4.0 1.3 - - - -
64A MET 3.8 0.7 - - - +
65A LEU* 3.3 8.0 - - - +
66A ASN* 2.7 47.7 + - - +
68A ASN* 5.1 2.5 + - - -
122A LEU* 4.2 1.9 + - - +
123A CYS* 1.3 76.7 - - - +
125A ALA* 1.3 61.7 + - - -
126A ILE* 5.0 2.7 - - - -
134A ILE* 5.9 1.6 - - - -
135A GLU 3.3 9.4 - - - -
136A GLU* 4.2 8.5 - - - -
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.9 15.3 - - + +
56A LEU* 4.3 12.8 - - + -
63A LEU* 4.8 12.1 - - + -
64A MET 3.4 5.6 - - - +
65A LEU* 4.1 13.9 - - + -
124A GLY* 1.3 75.1 - - - -
126A ILE* 1.3 62.2 + - - +
133A LYS 3.8 0.9 - - - +
134A ILE* 3.4 4.5 - - - +
135A GLU* 2.7 39.1 + - + +
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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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62A ASP 4.5 0.7 - - - +
63A LEU* 3.6 9.0 - - - -
64A MET* 2.7 65.6 + - + +
66A ASN* 3.3 36.1 - - + +
124A GLY 4.8 2.7 - - - +
125A ALA* 1.3 81.4 - - - +
127A SER* 1.3 70.1 + - - +
128A LEU* 4.1 3.5 + - + -
132A LEU* 4.1 18.4 - - + -
133A LYS 3.4 6.1 - - - +
134A ILE* 4.0 20.4 - - + -
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Residues in contact with SER 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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62A ASP* 4.5 8.4 + - - -
63A LEU* 3.8 22.4 - - - +
126A ILE* 1.3 77.2 - - - +
128A LEU* 1.3 59.8 + - - +
129A HIS 3.4 18.9 + - - -
131A LYS 3.2 3.9 + - - +
132A LEU* 3.5 4.0 - - - +
133A LYS* 2.8 54.9 + - - +
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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