Contacts of the strand formed by residues 95 - 102 (chain B) in PDB entry 3SKU
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 LEU 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLN* 5.7 0.7 - - - +
93B TYR* 3.7 21.5 - - + -
94B ASN* 1.3 73.6 - - - +
96B THR* 1.3 77.7 + - - +
97B ILE* 3.9 12.1 - - + -
114B GLU* 3.6 0.5 - - - +
115B TYR* 2.9 68.0 + - + +
124B LEU* 3.9 24.5 - - + -
125B GLY* 4.4 7.0 - - - +
168B VAL* 3.7 23.6 - - + -
169B LYS 3.4 2.5 - - - +
170B ILE* 3.5 26.7 - - + +
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Residues in contact with THR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN* 4.5 9.2 - - - +
45B PRO* 4.3 23.3 - - + -
94B ASN* 4.7 1.6 + - - +
95B LEU* 1.3 82.1 + - - +
97B ILE* 1.3 71.7 + - - +
98B ALA* 4.9 0.2 - - + -
112B VAL* 4.6 5.4 - - + -
113B MET 3.3 12.8 - - - +
114B GLU* 4.0 28.4 + - + +
167B LEU* 3.5 2.3 - - - +
168B VAL* 3.5 3.8 - - - -
169B LYS* 2.8 49.3 + - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 3.9 25.6 - - + -
96B THR* 1.3 78.5 - - - +
98B ALA* 1.3 65.7 + - - +
99B TRP* 4.6 17.5 - - + +
111B THR* 3.9 1.6 - - - +
112B VAL* 3.7 2.8 + - - -
113B MET* 2.8 48.7 + - + +
115B TYR* 3.9 15.5 - - + +
148B ASN* 3.7 29.2 - - + +
149B LEU* 4.3 20.0 - - + -
166B ARG* 4.8 5.4 - - + -
167B LEU 3.1 10.3 - - - +
168B VAL* 4.2 13.0 - - + -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 6.1 0.2 - - + -
45B PRO* 4.1 17.9 - - + -
96B THR* 4.9 3.1 - - + -
97B ILE* 1.3 76.1 - - - +
99B TRP* 1.3 63.6 + - - +
100B PHE* 3.3 25.9 - - + -
111B THR 3.5 5.8 - - - +
112B VAL* 5.2 6.1 - - + -
165B LEU 3.5 1.0 - - - +
166B ARG* 3.3 5.5 - - - -
167B LEU* 2.7 47.3 + - + +
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Residues in contact with TRP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 3.6 29.8 - - + -
97B ILE* 4.6 11.2 - - + +
98B ALA* 1.3 75.8 - - - +
100B PHE* 1.3 64.3 + - - +
109B PRO* 3.6 2.4 - - - +
110B ILE* 2.7 32.7 + - + -
111B THR* 2.8 40.7 + - + +
144B VAL* 5.1 5.2 - - + +
148B ASN 5.5 0.2 + - - -
149B LEU 4.0 12.8 + - - -
150B GLY 4.5 2.6 + - - -
151B PHE* 3.4 47.1 - + + +
164B TYR* 4.6 6.3 - + + -
165B LEU 3.4 22.0 - - - -
166B ARG* 3.5 36.2 - - + +
179B PHE* 3.4 37.0 - + - -
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.1 8.5 - - + -
45B PRO* 4.2 13.2 - - + -
47B PRO* 3.8 27.6 - - + -
98B ALA* 3.3 35.2 - - + -
99B TRP* 1.3 76.3 - - - +
101B ARG* 1.3 61.8 + - - +
102B MET* 3.3 13.8 + - - +
107B ALA* 4.0 9.6 - - + -
108B ILE 2.9 20.6 - - - +
109B PRO* 4.0 10.8 - - + -
110B ILE* 3.9 4.1 - - - +
112B VAL* 6.4 0.2 - - + -
164B TYR* 3.6 3.2 - - - -
165B LEU* 3.1 49.2 + - + +
166B ARG 5.3 0.2 - - - -
167B LEU* 4.4 8.3 - - + -
208B TYR* 3.7 28.0 - + - -
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 1.3 68.6 - - - +
102B MET* 1.3 77.1 + - - +
108B ILE* 3.0 51.7 + - + +
110B ILE* 3.5 14.6 - - + +
138B TYR* 3.4 29.3 + - + +
159B GLU* 2.9 30.2 + - - +
161B ALA 3.3 16.5 + - - -
162B GLY* 3.7 12.0 - - - -
163B THR 3.8 5.6 - - - -
164B TYR* 3.6 27.1 + - + -
195B LEU* 3.9 11.5 - - - +
197B ILE* 5.7 1.8 - - + +
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Residues in contact with MET 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PRO* 5.8 1.6 - - + -
48B PHE* 4.7 15.5 - - + -
100B PHE* 3.8 13.9 - - - +
101B ARG* 1.3 94.5 + - - +
103B GLY* 1.3 63.0 + - - +
106B CYS 3.7 14.4 - - - +
107B ALA* 4.3 11.4 - - + -
108B ILE* 4.8 3.1 - - - +
163B THR* 2.9 47.0 + - + +
164B TYR 4.3 0.9 - - - +
165B LEU* 3.8 41.5 - - + -
202B CYS* 5.1 1.1 - - - -
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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