Contacts of the strand formed by residues 94 - 102 (chain L) in PDB entry 1S5E
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 HIS 94 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16L GLN* 4.0 5.5 + - - -
18L HIS* 3.2 31.9 + + - -
47L THR 4.0 3.9 + - - +
48L PHE* 3.4 19.3 - + + +
49L GLN 3.0 23.0 + - - -
87L VAL* 3.8 17.3 - - + -
88L TRP 3.6 8.1 - - - +
89L ASN* 3.6 32.5 - - + +
91L LYS 3.1 16.7 + - - -
92L THR* 5.8 0.9 - - - -
93L PRO* 1.3 73.5 - - - +
95L ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L GLN* 3.4 11.2 - - + +
51L GLU* 3.6 40.2 - - + +
87L VAL* 3.1 4.9 - - - -
88L TRP* 2.8 48.4 + - + +
91L LYS* 4.2 10.7 - - + +
93L PRO 3.5 0.6 + - - -
94L HIS* 1.3 72.9 - - - +
96L ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L ILE* 3.9 12.3 - - + -
48L PHE* 3.8 27.8 - - + -
49L GLN 2.9 22.8 + - - +
50L VAL* 4.6 7.7 - - + +
51L GLU 5.7 0.9 + - - -
68L MET* 4.0 25.6 - - + -
72L LEU* 3.7 27.4 - - + -
85L LEU* 4.2 17.0 - - + -
86L CYS 3.8 4.0 - - - +
87L VAL* 4.3 5.4 - - + -
88L TRP* 3.5 11.0 - - - -
95L ALA* 1.3 71.0 - - - +
97L ALA* 1.3 59.0 + - - +
98L ALA 3.8 21.8 - - - +
31M LEU* 3.5 15.8 - - - +
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Residues in contact with ALA 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L LEU* 5.8 0.2 - - + -
12L TYR* 6.3 0.9 - - + -
15L THR* 5.0 0.9 - - - +
68L MET* 4.3 0.6 - - - +
86L CYS* 2.8 28.3 + - - +
87L VAL* 4.7 0.7 - - - +
88L TRP* 3.5 39.5 - - + -
95L ALA 3.5 1.6 + - - -
96L ILE* 1.3 73.3 - - - +
98L ALA* 1.3 62.3 + - + +
30M SER* 3.4 1.4 + - - -
31M LEU* 2.8 33.1 + - - +
32M ALA* 3.5 11.3 + - + -
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Residues in contact with ALA 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ILE* 3.7 16.2 - - + -
8L LEU* 3.9 20.2 - - + -
68L MET* 4.0 2.9 - - - -
85L LEU* 3.5 7.1 - - - +
86L CYS* 2.9 31.8 + - + +
96L ILE* 3.8 5.9 - - - +
97L ALA* 1.3 82.1 - - - +
99L ILE* 1.3 61.5 + - - +
28M THR* 5.3 1.8 - - + -
29M GLU 3.1 14.8 - - - +
30M SER* 3.8 7.2 - - - -
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Residues in contact with ILE 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ILE* 3.6 4.5 - - - -
24L ILE* 5.3 0.2 - - + -
40L ILE* 6.0 0.2 - - + -
68L MET* 3.9 21.8 - - + -
71L THR* 4.4 13.0 - - + -
72L LEU* 3.7 25.4 - - + -
75L ALA* 5.3 2.9 - - + -
82L VAL* 4.0 24.0 - - + -
84L LYS 3.5 6.7 - - - +
85L LEU* 3.7 17.3 - - + -
98L ALA* 1.3 73.5 - - - +
100L SER* 1.3 71.1 + - - +
101L MET* 4.2 17.7 - - + -
27M TYR* 4.0 1.5 - - + +
28M THR* 3.2 3.8 - - - +
29M GLU* 2.9 46.5 + - + +
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Residues in contact with SER 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ILE* 3.7 13.9 - - - +
82L VAL* 3.7 5.0 - - - +
83L GLU* 2.7 55.5 + - - -
84L LYS* 2.9 28.1 + - - +
99L ILE* 1.3 74.5 - - - +
101L MET* 1.3 58.3 + - - +
26M SER* 6.1 1.3 - - - -
27M TYR 3.4 4.5 - - - -
28M THR* 3.4 20.0 - - - -
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Residues in contact with MET 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L THR* 3.9 22.2 - - + +
75L ALA* 4.0 16.4 - - + -
80L ALA* 3.8 25.1 - - - -
81L LYS 3.5 17.0 - - - +
82L VAL* 4.3 3.8 - - + -
83L GLU* 4.6 0.2 - - - -
99L ILE* 4.2 17.0 - - + -
100L SER* 1.3 77.2 - - - +
102L ALA* 1.3 62.5 + - - +
26M SER* 3.2 7.3 - - - -
27M TYR* 2.8 59.2 + - + +
73M ARG* 5.3 2.2 - - + -
76M TYR* 3.5 24.4 + - + -
77M LEU* 4.5 10.8 - - + -
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Residues in contact with ALA 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L LYS* 3.5 20.2 + - - +
83L GLU* 4.3 25.8 + - + +
101L MET* 1.3 76.6 - - - +
103L ASN* 1.3 85.6 + - - +
25M PHE* 3.8 14.4 - - + +
26M SER* 3.9 15.9 - - - -
76M TYR* 3.3 8.4 + - - -
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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