Contacts of the strand formed by residues 101 - 112 (chain L) in PDB entry 5OA3
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 ARG 101 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6602 C 3.5 29.0 + - - -
11572 G 5.2 3.2 + - - -
95L TYR* 3.6 4.0 - - - -
96L ILE* 3.0 31.3 + - - +
99L TYR* 3.0 27.9 + - + +
100L ASN* 1.3 75.6 - - - +
102L PHE* 1.3 65.6 + - - +
77W PRO* 4.7 1.6 - - - +
79W PHE* 3.7 26.3 - - - -
4X CYS 3.9 4.8 + - - -
5X ARG* 2.5 55.1 + - - +
6X GLY 3.1 13.6 + - - -
7X LEU* 3.0 23.6 - - - +
9X THR* 3.9 9.1 - - + +
10X ALA* 3.9 12.6 - - + -
13X LEU* 4.4 10.1 - - + +
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Residues in contact with PHE 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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8022 A 5.4 7.4 - - - -
8032 C 5.0 15.7 - - - -
8542 A 6.0 2.0 - - - -
93L LEU* 3.6 42.6 - - + -
94L HIS 3.3 2.9 - - - +
95L TYR* 3.2 47.8 - + + -
100L ASN 5.9 0.9 - - - -
101L ARG* 1.3 76.8 - - - +
103L GLU* 1.3 61.5 + - - +
80W ASP* 4.2 22.7 - - - -
7X LEU* 3.2 29.2 + - + +
8X ARG* 3.1 31.7 - - + -
10X ALA* 3.3 6.1 - - - +
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Residues in contact with GLU 103 (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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93L LEU* 3.4 5.7 - - - -
94L HIS* 2.9 55.0 + - + +
96L ILE* 3.3 28.8 - - + +
102L PHE* 1.3 74.2 - - - +
104L LYS* 1.3 63.4 + - - +
105L ARG* 3.6 9.3 + - - +
8X ARG* 4.0 5.2 - - - +
10X ALA* 3.8 12.1 - - + -
11X ARG* 3.0 52.4 + - + +
14X ARG* 3.4 18.4 + - - -
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Residues in contact with LYS 104 (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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3992 C 3.0 46.6 - - + +
6802 G 5.5 0.7 - - - +
6812 U 2.6 32.0 + - - +
91L ASP* 4.4 11.7 - - + +
92L TYR 3.6 9.4 - - - +
93L LEU* 3.6 17.9 - - + +
103L GLU* 1.3 73.8 - - - +
105L ARG* 1.3 66.1 + - - +
8X ARG* 2.8 45.1 + - - +
11X ARG* 3.0 25.4 + - - +
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Residues in contact with ARG 105 (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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3552 G 2.7 47.8 + - - -
3562 C 2.9 29.5 + - - -
3992 C 2.9 9.4 - - - +
4002 C 5.2 7.9 + - - +
91L ASP* 3.4 5.2 - - - +
92L TYR* 2.9 57.5 + - + +
94L HIS* 3.1 36.3 + - + -
103L GLU* 3.6 16.6 + - + +
104L LYS* 1.3 78.8 - - - +
106L HIS* 1.3 59.3 + - - +
11X ARG* 4.5 11.9 - - - +
14X ARG* 4.9 4.9 - - - +
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Residues in contact with HIS 106 (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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3972 G 3.2 15.9 + - - -
3982 A 4.5 8.3 - - - -
3992 C 3.2 34.2 + - + +
89L ARG* 3.0 42.4 + - + +
90L ARG 3.2 9.4 - - - +
91L ASP* 3.6 19.7 - - - +
92L TYR* 4.1 1.1 + - - -
105L ARG* 1.3 78.1 - - - +
107L LYS* 1.3 71.4 + - - +
108L ASN* 3.1 29.1 + - - -
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Residues in contact with LYS 107 (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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3542 U 3.1 55.0 + - - +
3552 G 2.7 31.3 + - - -
89L ARG* 3.4 2.3 - - - -
90L ARG* 2.9 40.0 + - + +
92L TYR* 3.6 16.6 - - + +
106L HIS* 1.3 80.4 - - - +
108L ASN* 1.3 64.2 + - - +
109L MET* 3.8 5.1 + - + +
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Residues in contact with ASN 108 (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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3962 U 3.1 27.8 + - - +
3972 G 3.1 24.5 + - - +
13I LYS* 2.3 33.2 + - - +
78L THR* 4.6 3.3 + - - +
87L VAL* 3.8 9.3 - - + +
88L ILE 3.5 5.2 - - - +
89L ARG* 3.4 21.7 + - - +
106L HIS* 3.1 29.1 + - - -
107L LYS* 1.3 73.7 - - - +
109L MET* 1.3 56.4 + - - +
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Residues in contact with MET 109 (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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3532 C 4.0 24.9 - - - +
13I LYS* 3.9 1.3 - - - +
73L LEU* 4.2 11.4 - - + -
87L VAL* 3.5 3.2 - - - -
88L ILE* 2.9 58.8 + - + +
90L ARG* 3.9 22.4 - - - -
107L LYS* 3.8 5.6 + - + +
108L ASN* 1.3 72.3 - - - +
110L SER* 1.3 66.4 + - - +
111L VAL* 3.8 3.0 + - + -
128L VAL* 4.4 6.1 - - + -
140L PHE* 3.6 46.0 - - + -
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Residues in contact with SER 110 (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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3722 U 5.4 0.5 + - - -
3952 G 4.6 7.1 + - - -
3962 U 5.0 0.2 + - - -
13I LYS* 3.7 21.5 + - - +
82L MET* 4.5 14.8 - - - +
86L ILE 3.5 7.4 - - - -
87L VAL* 4.1 13.8 - - - +
109L MET* 1.3 78.4 - - - +
111L VAL* 1.3 60.0 - - - +
137L THR* 3.9 33.9 + - - +
138L VAL* 4.2 16.8 - - - +
139L ARG 4.6 2.8 + - - -
140L PHE* 4.8 3.6 - - - +
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Residues in contact with VAL 111 (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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85L THR* 3.0 5.5 + - - -
86L ILE* 2.9 55.9 + - + +
88L ILE* 3.9 22.4 - - + -
109L MET* 4.2 7.6 - - + +
110L SER* 1.3 77.5 - - - +
112L HIS* 1.3 67.9 + - - +
128L VAL* 4.3 8.3 - - + -
138L VAL* 4.3 5.8 - - - -
140L PHE* 3.6 12.1 - - + -
141L ASN* 3.6 34.3 - - - +
142L VAL* 4.1 7.9 - - + -
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Residues in contact with HIS 112 (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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3742 G 4.7 8.5 - - - -
57L ASP* 2.9 32.2 + - - -
59L LYS* 3.7 34.4 + - + +
60L CYS* 3.9 2.5 - - - -
84L ARG* 2.9 32.2 + - + +
85L THR* 4.0 4.3 - - - -
111L VAL* 1.3 77.7 - - - +
113L LEU* 1.3 72.8 + - - +
114L SER* 3.8 4.9 - - - -
134L LEU* 4.0 14.6 - - + -
138L VAL* 3.9 8.0 - - + +
140L PHE 3.5 15.0 + - - +
141L ASN* 3.2 25.7 + - - +
142L VAL* 3.1 21.4 + - - +
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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