Contacts of the strand formed by residues 117 - 125 (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 GLY 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A MET* 3.8 5.6 - - - -
116A GLN* 1.3 80.9 - - - +
118A THR* 1.3 65.6 + - - -
119A ILE* 4.8 3.8 - - - +
195A LEU 4.0 0.5 - - - +
197A ALA* 2.8 36.3 + - - +
223A PHE* 4.8 0.4 - - - -
258A TYR 3.1 13.2 - - - -
259A SER 3.5 10.3 - - - -
260A ASN 3.7 4.3 - - - -
261A ALA* 4.6 0.5 - - - -
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Residues in contact with THR 118 (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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114A MET* 4.4 0.8 - - - +
117A GLY* 1.3 74.9 + - - -
119A ILE* 1.3 72.6 + - - +
120A ILE* 4.2 1.3 - - + +
194A ALA* 5.0 0.2 - - + -
195A LEU 3.3 12.1 - - - +
196A LYS* 4.4 2.5 - - - +
256A LYS 3.7 1.0 - - - +
257A VAL* 3.4 3.5 - - - +
258A TYR* 2.8 46.8 + - + +
260A ASN 2.8 22.0 + - - -
261A ALA* 3.4 2.4 - - - -
262A LEU* 3.0 23.7 + - + -
267A LEU* 3.8 37.7 - - + -
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Residues in contact with ILE 119 (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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114A MET* 4.8 6.1 - - + -
117A GLY 4.8 0.2 - - - -
118A THR* 1.3 85.1 - - - +
120A ILE* 1.3 62.9 + - - +
121A LEU* 3.9 14.1 - - + +
135A PHE* 4.0 26.7 - - + -
149A PHE* 4.3 8.5 - - + -
151A ILE* 3.7 22.5 - - + +
194A ALA* 3.0 6.2 - - - +
195A LEU* 2.8 48.2 + - + +
223A PHE* 4.1 27.4 - - + -
255A ILE* 4.2 11.2 - - + -
256A LYS 3.5 7.6 - - - +
257A VAL* 4.2 11.9 - - + -
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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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118A THR* 5.4 0.7 - - + -
119A ILE* 1.3 74.8 - - - +
121A LEU* 1.3 65.2 + - - +
192A THR* 4.1 19.7 - - + -
193A VAL 3.3 11.9 - - - +
194A ALA* 4.1 7.2 - - + -
254A ASP* 4.5 1.4 - - - +
255A ILE* 3.2 2.6 - - - +
256A LYS* 2.9 60.0 + - + +
258A TYR* 3.9 14.4 - - + +
262A LEU* 5.6 0.9 - - + -
267A LEU* 4.9 8.3 - - + -
270A ALA* 3.3 35.4 - - + +
271A THR* 4.4 4.3 - - + -
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Residues in contact with LEU 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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119A ILE* 3.9 20.0 - - + +
120A ILE* 1.3 78.9 - - - +
122A SER* 1.3 62.7 + - - +
123A TYR* 4.1 2.5 + - + -
134A LEU* 3.6 39.5 - - + +
135A PHE* 4.3 7.0 - - + -
151A ILE* 4.4 12.6 - - + -
191A ASN 3.7 1.0 - - - +
192A THR* 3.4 5.6 - - - -
193A VAL* 2.9 56.8 + - + +
235A LEU* 5.1 0.2 - - + -
252A ILE* 4.2 22.0 - - + -
254A ASP 3.1 14.1 - - - +
255A ILE* 3.9 11.0 - - + -
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Residues in contact with SER 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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121A LEU* 1.3 71.4 - - - +
123A TYR* 1.3 56.9 + - - +
190A PHE* 3.4 23.8 - - - +
191A ASN 3.2 8.7 + - - -
192A THR* 4.2 14.7 + - - +
252A ILE* 3.4 4.5 - - - +
253A GLY* 2.7 29.5 + - - -
254A ASP* 2.9 25.6 + - - +
274A THR* 5.2 1.2 - - - +
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Residues in contact with TYR 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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121A LEU* 4.5 5.2 - - + -
122A SER* 1.3 78.4 + - - +
124A LYS* 1.3 62.6 + - - +
125A SER* 3.7 17.0 - - - -
134A LEU* 3.9 21.3 - - + -
153A ILE* 3.5 27.1 - - + +
180A VAL* 3.3 34.8 - - - +
181A ARG 4.5 2.2 + - - -
189A VAL 3.9 0.3 - - - +
190A PHE* 3.1 7.4 - - - -
191A ASN* 2.8 62.5 + - + +
193A VAL* 3.8 19.7 - - + -
248A PHE* 3.8 12.3 - + + -
251A THR 3.2 11.9 - - - +
252A ILE* 3.9 18.4 - - + -
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Residues in contact with LYS 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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123A TYR* 1.3 76.5 - - - +
125A SER* 1.3 60.3 + - - +
126A THR* 4.6 10.1 - - + -
188A ARG* 3.7 39.9 - - + +
189A VAL 3.9 12.8 - - - +
190A PHE* 3.8 37.9 - - + -
248A PHE* 3.4 1.8 - - - -
250A GLY* 3.2 4.7 - - - -
251A THR* 2.8 52.3 + - - +
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Residues in contact with SER 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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123A TYR* 3.7 8.6 - - - -
124A LYS* 1.3 73.9 - - - +
126A THR* 1.3 62.8 + - - +
127A SER 3.5 5.9 + - - -
132A GLN* 2.7 37.0 + - - -
153A ILE* 4.0 15.9 - - - -
182A ALA* 4.8 9.3 - - - +
188A ARG* 2.8 29.8 + - - +
189A VAL 4.9 1.6 + - - -
191A ASN* 5.8 0.2 + - - -
248A PHE* 3.8 10.5 - - - -
249A GLY 3.4 4.5 - - - -
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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