Contacts of the strand formed by residues 148 - 155 (chain A) in PDB entry 3SXW
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 PHE 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A HIS 3.6 2.1 - - - +
74A VAL* 3.6 0.3 - - - -
75A ILE* 2.8 46.9 + - + +
103A ALA* 4.3 6.5 - - + -
105A LYS 3.3 16.4 - - - -
106A GLY* 4.3 1.8 - - - -
107A LYS 3.9 6.1 - - - +
108A GLY* 3.6 21.3 - - - -
109A GLY 3.5 26.0 - - - -
124A SER* 3.3 33.4 - - - -
140A ALA* 4.1 4.7 - - + -
141A VAL 3.4 18.2 - - - -
142A ASN* 3.3 25.0 - - + +
147A PRO* 1.3 71.9 - - - +
149A ILE* 1.3 59.3 + - - +
150A MET* 3.5 32.3 - - + -
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Residues in contact with ILE 149 (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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13A ASP 5.3 0.2 - - - +
14A PHE 3.7 12.8 - - - +
15A GLU 3.5 24.2 - - - +
16A THR* 3.6 20.0 - - - +
17A GLY* 3.7 16.6 - - - +
72A THR* 4.6 2.2 - - - -
73A HIS 3.3 7.4 - - - +
74A VAL* 4.0 18.2 - - + -
103A ALA* 3.8 1.6 - - - +
104A LEU* 2.8 45.8 + - + -
105A LYS* 2.9 27.2 + - + +
147A PRO* 4.4 8.5 - - + -
148A PHE* 1.3 79.3 - - - +
150A MET* 1.3 69.4 + - - +
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Residues in contact with MET 150 (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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72A THR* 3.1 6.8 - - - -
73A HIS* 2.8 37.3 + - + +
75A ILE* 6.2 0.4 - - + -
101A ALA* 3.6 25.4 - - + +
102A VAL 3.3 5.8 - - - +
103A ALA* 3.9 17.9 - - - +
104A LEU* 4.4 4.7 - - - +
110A VAL* 3.6 27.4 - - + -
124A SER* 3.7 19.7 - - - +
130A ILE* 4.0 6.3 - - + -
140A ALA* 4.1 13.0 - - + -
148A PHE* 3.5 31.6 - - + -
149A ILE* 1.3 75.6 - - - +
151A LEU* 1.3 59.8 + - - +
152A VAL* 4.0 12.9 + - + -
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Residues in contact with LEU 151 (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 VAL* 4.9 12.6 - - + -
14A PHE* 6.2 2.9 - - + -
19A ILE* 5.2 0.2 - - + -
70A PHE* 4.2 22.2 - - + -
71A SER 3.2 21.5 - - - +
72A THR* 4.1 10.8 - - + -
100A VAL 3.8 1.4 - - - +
101A ALA* 3.3 1.9 - - - -
102A VAL* 2.7 50.3 + - + +
104A LEU* 3.9 22.0 - - + +
150A MET* 1.3 71.0 - - - +
152A VAL* 1.3 59.8 + - - +
153A ILE* 3.9 18.5 - - + +
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Residues in contact with VAL 152 (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 PHE* 3.1 4.7 - - - +
71A SER* 2.7 44.9 + - - +
73A HIS* 4.0 36.1 - - + +
99A GLN* 3.8 24.5 - - + +
100A VAL 3.4 9.4 - - - +
101A ALA* 4.2 14.6 - - + -
150A MET* 4.4 10.8 - - + +
151A LEU* 1.3 77.1 - - - +
153A ILE* 1.3 67.0 + - - +
154A TYR* 3.8 16.0 - - + -
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Residues in contact with ILE 153 (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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68A LEU* 4.5 27.4 - - + -
69A ASN 3.4 10.5 - - - +
70A PHE* 4.0 12.6 - - + -
99A GLN* 3.5 2.3 - - - +
100A VAL* 2.8 50.6 + - + +
102A VAL* 4.5 10.1 - - + -
151A LEU* 3.9 30.5 - - + +
152A VAL* 1.3 77.5 - - - +
154A TYR* 1.3 68.2 + - - +
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Residues in contact with TYR 154 (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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58A ALA* 4.1 10.4 - - - +
60A GLU* 2.7 31.5 + - - +
68A LEU* 3.7 6.5 - - - -
69A ASN* 2.8 58.7 + - + +
70A PHE* 4.1 2.1 + - - -
71A SER* 3.6 22.0 + - - -
73A HIS* 5.9 0.7 - - - -
90A HIS* 6.1 1.6 - - - -
92A HIS* 4.4 11.7 - + - +
98A ALA 4.3 0.7 - - - +
99A GLN* 4.1 14.1 - - + -
152A VAL* 3.8 18.2 - - + -
153A ILE* 1.3 79.8 - - - +
155A PRO* 1.3 83.7 - - + +
158A ALA* 4.8 6.7 - - + -
159A GLY 5.9 1.3 - - - -
160A HIS* 4.5 18.1 + + - -
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Residues in contact with PRO 155 (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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66A GLY 6.1 1.6 - - - +
67A ASP 3.6 9.6 - - - +
68A LEU* 4.2 8.7 - - + -
69A ASN* 4.4 0.3 + - - -
97A ARG* 3.6 34.1 - - + -
98A ALA 3.0 25.6 - - - +
154A TYR* 1.3 95.2 - - + +
156A ALA* 1.3 65.6 + - - +
157A ASP* 3.1 8.7 - - - +
158A ALA* 3.1 19.2 + - + +
159A GLY 4.8 0.3 + - - -
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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