Contacts of the strand formed by residues 131 - 138 (chain A) in PDB entry 1SLL
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 ILE 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ASN* 4.5 2.1 - - - +
130A GLY* 1.3 79.6 - - - +
132A GLN* 1.3 66.3 + - - +
150A HIS* 4.9 1.3 - - - +
152A TYR* 3.9 29.4 - - + -
153A ILE 3.6 2.9 - - - -
154A THR* 4.6 11.2 - - + -
246A TYR* 3.2 58.0 - - + -
247A PRO* 3.8 4.7 - - - +
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Residues in contact with GLN 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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125A SER* 2.7 22.3 + - - -
127A SER* 2.9 33.8 + - - -
129A ASN* 2.9 25.5 + - + +
131A ILE* 1.3 76.2 - - - +
133A SER* 1.3 63.0 + - - +
134A LEU* 3.5 0.9 + - - +
152A TYR* 3.2 4.8 - - - -
153A ILE* 2.8 56.6 + - + +
155A ASN* 4.6 7.1 - - - +
246A TYR 3.5 4.3 - - - -
247A PRO 3.5 14.1 - - - +
248A PHE* 3.4 23.9 - - + -
249A GLY 3.5 8.3 + - - -
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Residues in contact with SER 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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132A GLN* 1.3 70.9 - - - +
134A LEU* 1.3 61.0 + - - +
135A PHE 4.6 2.5 - - - -
150A HIS* 2.8 20.5 - - - -
151A ILE 3.6 6.5 - - - -
152A TYR* 3.8 2.9 - - - -
236A GLY* 3.0 24.6 - - - -
237A GLY* 3.5 28.0 - - - -
238A THR* 2.7 21.6 + - - -
246A TYR* 2.8 19.4 + - - +
248A PHE* 3.3 5.9 - - - +
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Residues in contact with LEU 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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121A LEU* 3.6 21.5 - - + +
123A TYR* 3.9 24.9 - - + -
132A GLN 3.5 1.3 + - - +
133A SER* 1.3 74.4 - - - +
135A PHE* 1.3 61.1 + - - +
151A ILE* 2.8 22.8 + - + +
152A TYR 4.6 0.9 - - - -
153A ILE* 3.6 45.3 - - + -
159A ILE* 5.3 0.4 - - + -
193A VAL* 4.1 17.3 - - + -
235A LEU* 3.5 11.6 - - - +
236A GLY* 2.9 21.1 + - - +
248A PHE* 3.7 28.3 - - + -
252A ILE* 4.2 7.9 - - + +
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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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87A MET* 5.0 0.4 - - - -
102A LEU* 4.3 4.3 - - + -
111A VAL* 3.9 13.0 - - + -
114A MET* 6.1 0.2 - - - -
119A ILE* 4.0 29.2 - - + -
121A LEU* 4.3 6.5 - - + -
133A SER* 3.6 0.4 - - - -
134A LEU* 1.3 83.3 - - + +
136A SER* 1.3 63.5 + - - +
137A VAL* 3.5 28.7 - - + -
149A PHE* 4.1 18.4 - + - -
150A HIS* 3.2 4.3 - - - +
151A ILE* 3.0 31.7 + - + -
224A ILE* 5.3 1.8 - - + -
233A VAL* 3.6 22.2 - - + -
234A THR 3.4 11.0 - - - -
235A LEU* 4.0 6.5 - - + -
237A GLY 4.9 1.3 - - - -
255A ILE* 3.4 31.9 - - + -
257A VAL* 4.2 13.0 - - + -
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Residues in contact with SER 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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135A PHE* 1.3 78.5 - - - +
137A VAL* 1.3 70.4 + - - +
138A GLY 4.4 0.2 - - - -
148A HIS* 5.7 0.2 - - - -
149A PHE 3.1 13.9 - - - -
150A HIS* 3.5 1.3 - - - -
232A ASN* 4.6 1.8 + - - -
233A VAL* 3.5 1.7 - - - +
234A THR* 2.8 42.8 + - - +
237A GLY 2.6 23.0 + - - -
238A THR* 3.4 31.9 - - - -
239A LYS 4.5 0.9 + - - -
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Residues in contact with VAL 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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111A VAL* 3.8 14.4 - - + -
112A LYS* 4.0 10.3 - - + -
135A PHE* 3.5 28.9 - - + -
136A SER* 1.3 80.6 - - - +
138A GLY* 1.3 62.3 + - - +
148A HIS* 3.5 1.9 - - - -
149A PHE* 2.8 32.5 + - + +
224A ILE* 3.5 35.0 - - + -
227A ILE* 4.0 3.3 - - - +
230A VAL* 3.5 22.7 - - + -
232A ASN 3.4 9.0 - - - +
233A VAL* 4.0 5.2 - - + -
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Residues in contact with GLY 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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137A VAL* 1.3 76.8 - - - +
139A ASN* 1.3 59.0 + - - -
147A ARG 3.6 9.6 - - - -
148A HIS* 3.9 7.4 - - - -
227A ILE* 4.7 0.2 - - - -
230A VAL* 3.8 16.4 - - - -
231A ASP 2.8 17.0 + - - -
232A ASN* 2.7 34.5 + - - +
239A LYS 5.5 0.4 - - - -
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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