Contacts of the strand formed by residues 94 - 103 (chain A) in PDB entry 6P59
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 LYS 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.7 13.5 - - - +
91A GLU* 3.2 31.7 + - + +
92A ALA 3.3 5.1 - - - +
93A GLY* 1.3 82.1 + - - +
95A VAL* 1.3 63.7 + - - +
96A TYR* 4.1 34.8 + - + +
113A TRP* 3.8 45.0 - - + +
114A ILE 3.3 12.8 - - - +
115A ASP* 4.3 9.2 - - - +
116A LEU* 3.6 7.7 - - - +
118A ARG* 4.5 6.5 - - - +
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Residues in contact with VAL 95 (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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44A PHE* 3.6 28.9 - - + -
48A CYS* 4.9 3.1 - - - -
55A ILE* 5.7 0.2 - - + -
86A VAL* 3.7 29.6 - - + -
87A ASP 3.7 9.6 - - - +
88A LEU* 3.6 20.2 - - + -
94A LYS* 1.3 73.7 - - - +
96A TYR* 1.3 70.2 + - - +
97A LEU* 3.9 8.3 + - + +
113A TRP* 3.1 2.3 - - - -
114A ILE* 2.9 46.4 + - + +
116A LEU* 3.6 6.7 - - + -
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Residues in contact with TYR 96 (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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84A GLU 5.2 0.4 - - - +
85A TYR 3.9 0.3 - - - +
87A ASP* 3.0 40.9 + - + +
90A ARG* 3.4 56.1 - - + +
91A GLU* 2.7 39.6 + - + -
94A LYS* 4.1 24.5 + - + +
95A VAL* 1.3 78.7 - - - +
97A LEU* 1.3 65.0 + - - +
112A GLY 3.4 7.6 - - - -
113A TRP* 3.9 26.0 - + + -
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Residues in contact with LEU 97 (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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27A ILE* 4.5 11.7 - - + -
55A ILE* 4.4 0.2 - - + -
57A PHE* 3.4 46.2 - - + -
68A PHE* 4.2 11.9 - - + -
84A GLU 5.2 0.2 - - - -
85A TYR 3.2 4.9 - - - +
86A VAL* 4.0 22.2 - - + -
95A VAL* 3.9 19.3 - - + +
96A TYR* 1.3 85.1 - - - +
98A LYS* 1.3 62.3 - - - +
110A TRP* 4.3 11.0 - - + -
111A LYS* 3.2 8.2 - - - +
112A GLY 2.7 38.9 + - - +
114A ILE* 4.0 15.7 - - + -
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Residues in contact with LYS 98 (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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68A PHE* 3.7 3.3 - - - -
84A GLU* 3.8 46.9 + - + +
85A TYR* 2.7 47.8 + - + +
97A LEU* 1.3 74.5 - - - +
99A ALA* 1.3 65.2 + - - +
100A PRO* 4.7 9.2 - - + -
109A ILE* 4.1 26.5 - - + -
110A TRP 3.3 4.3 - - - -
111A LYS* 4.1 25.7 - - + +
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Residues in contact with ALA 99 (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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66A LEU* 4.5 4.7 - - + -
68A PHE* 4.2 6.5 - - + -
98A LYS* 1.3 78.0 - - - +
100A PRO* 1.3 66.4 - - - +
101A MET* 3.7 13.8 + - + +
109A ILE* 3.6 2.0 - - - -
110A TRP* 2.7 48.6 + - + +
8B VAL* 3.6 31.4 - - + -
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Residues in contact with PRO 100 (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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79A GLN* 3.8 13.2 - - - +
85A TYR* 3.3 42.4 - - + +
98A LYS* 4.7 7.9 - - + -
99A ALA* 1.3 85.1 - - - +
101A MET* 1.3 64.5 + - - +
108A VAL 3.5 9.9 - - - +
109A ILE* 4.3 19.3 - - + -
128A ASP* 4.7 4.3 - - - +
131A ARG* 3.6 17.1 + - - +
8B VAL* 4.2 7.6 - - + +
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Residues in contact with MET 101 (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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21A LEU* 5.0 3.1 - - + -
66A LEU* 3.5 30.1 - - + -
79A GLN* 5.0 8.3 - - - +
99A ALA* 3.9 11.7 - - + +
100A PRO* 1.3 76.1 - - - +
102A ILE* 1.3 65.3 + - - +
103A LEU* 3.4 28.5 - - + -
107A CYS* 3.9 0.3 - - - -
108A VAL* 2.9 37.4 + - + +
110A TRP* 4.0 27.1 - - + -
125A LEU* 4.9 0.2 - - + -
131A ARG* 3.5 10.2 + - - +
8B VAL* 4.9 7.6 - - - +
9B ARG* 5.0 0.7 - - - -
10B PRO* 3.6 27.6 - - + -
104B ASP* 4.4 11.0 - - - +
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Residues in contact with ILE 102 (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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78A ARG* 5.4 2.7 - - - +
79A GLN* 5.6 1.2 - - - +
101A MET* 1.3 78.5 - - - +
103A LEU* 1.3 61.6 + - - +
105A GLY* 3.7 26.5 - - - +
106A VAL 3.5 7.2 - - - +
107A CYS* 4.0 11.7 - - - +
131A ARG* 3.8 30.3 - - - +
136A ASP* 3.7 23.3 - - - +
101B TYR* 4.1 8.1 - - + +
102B PHE 3.4 21.5 - - - +
103B THR* 3.2 22.0 - - - +
104B ASP* 2.8 35.3 + - - +
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Residues in contact with LEU 103 (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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17A PHE* 3.9 13.5 - - + -
18A PHE* 3.5 41.7 - - + -
21A LEU* 3.9 24.5 - - + -
101A MET* 3.4 42.0 - - + -
102A ILE* 1.3 74.7 - - - +
104A ASN* 1.3 72.8 + - - +
105A GLY 3.2 0.2 - - - -
106A VAL* 2.8 28.3 + - - +
108A VAL* 3.6 19.5 - - + -
125A LEU* 4.4 2.5 - - + -
10B PRO* 4.6 8.7 - - + -
104B ASP 3.5 4.3 - - - -
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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