Contacts of the strand formed by residues 94 - 102 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J GLN* 3.7 9.2 + - - -
18J HIS* 3.0 33.5 + + - -
47J THR 4.1 3.9 + - - +
48J PHE* 3.4 22.3 - + + +
49J GLN 3.0 22.5 + - - -
87J VAL* 3.8 20.2 - - + -
88J TRP 3.6 2.5 - - - +
89J ASN* 3.4 31.1 - - + +
91J LYS 3.3 15.6 + - - -
92J THR* 4.0 3.0 + - - +
93J PRO* 1.3 71.8 - - - +
95J ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J GLN* 3.4 9.9 - - + +
51J GLU* 3.5 40.2 - - + +
87J VAL* 3.1 4.1 - - - -
88J TRP* 2.7 47.2 + - + +
91J LYS* 4.2 13.4 - - + +
93J PRO 3.4 0.4 + - - -
94J HIS* 1.3 71.8 - - - +
96J ILE* 1.3 65.1 + - - +
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Residues in contact with ILE 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J ILE* 3.9 13.5 - - + -
48J PHE* 3.9 28.0 - - + -
49J GLN 2.8 20.8 + - - +
50J VAL* 4.3 9.7 - - + +
51J GLU 5.7 0.5 + - - -
68J MET* 3.9 24.5 - - + -
72J LEU* 3.7 27.6 - - + -
85J LEU* 4.2 18.4 - - + -
86J CYS 3.8 3.8 - - - -
87J VAL* 4.3 2.9 - - + -
88J TRP* 3.2 11.9 - - - -
95J ALA* 1.3 72.9 - - - +
97J ALA* 1.3 60.3 + - - +
98J ALA 3.8 22.0 - - - +
31K LEU* 3.4 14.2 - - - +
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Residues in contact with ALA 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J THR* 5.0 1.6 - - + -
86J CYS* 2.8 28.2 + - - +
87J VAL* 4.6 1.3 - - - +
88J TRP* 3.4 39.0 - - + -
95J ALA 3.4 0.8 + - - -
96J ILE* 1.3 73.9 - - - +
98J ALA* 1.3 60.8 + - + +
30K SER* 3.4 0.9 + - - -
31K LEU* 2.8 37.1 + - - +
32K ALA* 3.5 11.5 + - + -
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Residues in contact with ALA 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J ILE* 3.7 9.6 - - + -
8J LEU* 3.7 28.9 - - + -
68J MET* 4.1 2.5 - - - -
85J LEU* 3.4 9.2 - - - +
86J CYS* 2.9 37.8 + - + +
96J ILE* 3.8 5.4 - - - +
97J ALA* 1.3 80.6 - - - +
99J ILE* 1.3 63.6 + - - +
28K THR* 5.2 1.1 - - + -
29K GLU 3.2 13.9 - - - +
30K SER* 3.9 1.1 - - - -
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Residues in contact with ILE 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J ILE* 3.7 4.5 - - - -
24J ILE* 5.6 0.4 - - + -
68J MET* 3.9 24.0 - - + -
71J THR* 4.4 12.3 - - + -
72J LEU* 3.8 26.2 - - + -
75J ALA* 5.6 1.1 - - + -
82J VAL* 4.0 25.6 - - + -
84J LYS 3.6 6.5 - - - +
85J LEU* 3.8 15.5 - - + -
98J ALA* 1.3 76.4 - - - +
100J SER* 1.3 72.7 + - - +
101J MET* 4.2 16.4 - - + -
27K TYR* 5.4 0.9 - - + +
28K THR* 3.1 5.4 - - - +
29K GLU* 2.9 44.6 + - + +
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Residues in contact with SER 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J ILE* 3.9 14.1 - - - +
82J VAL* 3.8 2.1 - - - -
83J GLU* 2.7 50.2 + - - -
84J LYS* 3.0 27.9 + - - +
99J ILE* 1.3 75.5 - - - +
101J MET* 1.3 65.3 + - - +
26K SER* 6.1 1.6 - - - -
27K TYR 3.4 4.5 - - - -
28K THR* 3.4 17.9 - - - -
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Residues in contact with MET 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J THR* 4.2 16.8 - - + -
75J ALA* 4.1 25.4 - - + -
80J ALA* 4.2 15.3 - - - -
81J LYS 3.7 15.3 - - - +
82J VAL* 4.4 4.3 - - + -
83J GLU 4.1 0.2 - - - +
99J ILE* 4.2 19.1 - - + -
100J SER* 1.3 79.2 - - - +
102J ALA* 1.3 62.3 + - - +
26K SER* 3.2 7.3 - - - -
27K TYR* 2.8 61.2 + - + +
73K ARG* 4.8 6.1 - - + -
76K TYR* 3.4 24.6 + - + -
77K LEU* 4.4 9.6 - - + -
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Residues in contact with ALA 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J ASN* 5.2 4.5 + - - -
81J LYS* 3.8 19.4 + - - +
83J GLU* 4.1 27.5 + - + +
101J MET* 1.3 76.3 - - - +
103J ASN* 1.3 63.9 + - - +
25K PHE* 3.7 28.3 - - + +
26K SER* 4.0 10.1 - - - -
76K TYR* 3.1 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