Contacts of the strand formed by residues 120 - 128 (chain D) in PDB entry 5SWW
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 120 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 3.8 19.5 - - + -
90D TYR* 3.4 5.6 - - + +
92D VAL* 3.7 27.6 - - + -
113D PHE* 3.7 32.5 - - + -
114D LEU* 3.9 15.7 - - + +
117D ASN* 3.4 15.8 + - + +
118D THR* 3.2 3.2 - - - +
119D HIS* 1.3 107.9 - - + +
121D ARG* 1.3 73.8 + - - +
122D LEU* 4.9 1.1 - - + +
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU* 5.9 1.8 - - + -
89D ILE* 5.2 14.1 - - + +
90D TYR 2.9 11.9 + - - +
91D ARG* 3.3 15.0 - - + +
92D VAL* 2.7 33.8 + - - +
114D LEU* 5.1 0.2 - - - -
118D THR* 3.2 36.8 + - - +
119D HIS 4.2 0.2 - - - -
120D VAL* 1.3 77.7 + - - +
122D LEU* 1.3 59.8 + - - +
123D ARG* 5.9 2.2 - - + -
147D GLY 4.6 14.3 + - - +
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D VAL* 3.4 34.1 - - + +
94D TRP* 3.9 26.9 - - + -
110D VAL* 3.7 30.3 - - + -
113D PHE* 6.2 1.1 - - + -
114D LEU* 3.9 20.8 - - + +
120D VAL* 4.2 2.6 + - + -
121D ARG* 1.3 77.6 - - - +
123D ARG* 1.3 75.5 + - - +
124D ILE* 3.7 22.7 - - + -
147D GLY 4.1 2.5 + - - +
148D ALA* 3.2 15.9 - - + +
149D GLN 3.1 18.9 + - - -
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Residues in contact with ARG 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLU* 4.8 2.8 + - - -
91D ARG* 3.6 46.0 - - + +
92D VAL 2.9 9.6 + - - +
93D THR* 2.9 36.0 + - - +
94D TRP* 2.9 28.6 + - - +
95D PHE* 5.9 0.2 - - - -
121D ARG* 5.5 2.7 - - + -
122D LEU* 1.3 79.1 - - - +
124D ILE* 1.3 62.9 + - - +
125D PHE* 4.4 16.3 - - + -
149D GLN* 3.4 38.8 + - + +
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Residues in contact with ILE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D TRP* 4.0 24.5 - - + -
96D ILE* 4.1 22.9 - - + -
100D PRO* 4.3 12.8 - - + -
122D LEU* 3.7 30.1 - - + -
123D ARG* 1.3 76.4 - - - +
125D PHE* 1.3 68.2 + - - +
126D ALA* 4.6 3.4 - - + +
143D LEU* 3.7 38.1 - - + -
148D ALA* 4.7 3.8 - - + -
149D GLN* 2.6 17.5 + - - +
150D VAL* 3.6 9.4 - - + -
151D SER* 3.0 27.7 + - - +
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Residues in contact with PHE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D THR* 4.0 18.2 - - + -
94D TRP 2.9 20.7 + - - +
95D PHE* 3.4 29.5 - + + -
96D ILE* 2.9 28.8 + - - +
123D ARG* 4.4 20.9 - - + -
124D ILE* 1.3 74.1 - - - +
126D ALA* 1.3 61.8 + - - +
149D GLN* 3.5 20.9 - - - -
151D SER* 3.6 30.3 - - - -
152D ILE 4.6 4.5 - - - -
153D MET* 3.8 10.7 - - + +
157D GLU* 3.9 28.0 - - + -
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ILE* 3.5 9.9 - - + -
99D SER* 4.0 24.2 - - - +
100D PRO* 5.3 0.4 - - + -
124D ILE* 4.0 4.6 - - + -
125D PHE* 1.3 71.0 - - - +
127D ALA* 1.3 63.5 + - - +
128D ARG 3.6 17.5 - - - +
140D LEU* 5.9 2.7 - - + -
150D VAL* 6.2 2.0 - - + -
151D SER 3.1 12.5 + - - +
152D ILE* 3.5 17.3 - - + +
153D MET* 2.9 21.0 + - - -
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Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D PHE* 4.0 31.2 - - + +
24D ASN* 3.3 23.0 + - + +
96D ILE 3.0 11.9 + - - +
97D SER* 3.7 10.3 - - - +
126D ALA* 1.3 73.3 - - - +
128D ARG* 1.3 62.6 + - + +
152D ILE* 4.8 2.6 - - - +
153D MET* 3.7 27.7 - - - +
158D PHE* 4.1 5.3 - - + -
186D LEU* 3.3 10.5 - - - +
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Residues in contact with ARG 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ASN* 2.4 26.4 + - - +
22D PHE* 4.2 0.8 - - - +
23D ASN 2.7 31.6 + - - +
24D ASN* 3.6 20.6 - - - +
25D GLY 5.2 0.7 - - - -
26D ILE 3.2 13.1 + - - -
27D GLY* 3.7 12.3 - - - +
28D ARG* 3.7 9.7 - - - +
30D LYS 4.3 2.4 + - - -
97D SER* 2.6 32.8 + - - +
98D TRP* 3.0 51.9 - - + +
99D SER 3.1 23.3 + - - -
126D ALA* 3.6 10.0 - - - +
127D ALA* 1.3 80.9 - - + +
129D ILE* 1.3 64.7 + - - +
152D ILE* 5.3 0.2 - - - -
186D LEU* 3.8 7.0 - - + -
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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