Contacts of the strand formed by residues 104 - 109 (chain L) in PDB entry 2A3W
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 ILE 104 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10K VAL* 3.9 28.3 - - + -
12K PRO* 3.9 16.6 - - + -
197K ILE* 4.2 11.2 - - + -
199K LYS* 4.1 15.7 - - + -
97L SER* 3.7 2.1 + - - +
98L TRP* 3.4 4.1 - - - -
99L GLU* 3.2 26.9 + - + +
102L SER* 3.1 29.1 + - - +
103L GLY* 1.3 75.6 - - - +
105L ALA* 1.3 63.9 + - - +
106L GLU* 4.3 11.2 - - + +
116L LYS* 3.9 29.6 - - + -
117L LYS 3.3 11.0 - - - +
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Residues in contact with ALA 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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73L LEU* 3.7 29.8 - - + -
80L VAL* 3.9 20.0 - - + -
96L VAL* 5.1 2.0 - - + -
97L SER 3.3 4.9 - - - +
98L TRP* 4.2 1.1 - - + -
103L GLY 3.4 1.4 + - - -
104L ILE* 1.3 73.9 - - - +
106L GLU* 1.3 60.8 + - - +
107L PHE* 4.1 4.3 + - + -
115L VAL 4.7 0.5 - - - +
116L LYS* 3.7 5.4 - - - -
117L LYS* 2.6 35.5 + - + +
119L LEU* 3.9 8.5 - - + -
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Residues in contact with GLU 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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199K LYS* 5.1 4.5 - - - +
202K VAL* 5.8 2.0 - - + +
95L CYS 3.8 0.2 - - - +
96L VAL* 3.1 8.0 - - - -
97L SER* 2.9 50.1 + - - +
104L ILE* 4.3 8.5 - - + +
105L ALA* 1.3 72.9 - - - +
107L PHE* 1.3 61.9 + - - +
108L TRP* 3.3 33.5 + - + +
114L LEU 5.7 2.0 - - - +
116L LYS* 3.2 46.6 + - + +
163L VAL* 4.7 10.7 - - - +
164L LEU 4.8 5.2 - - - +
166L PRO* 6.0 1.4 - - - +
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Residues in contact with PHE 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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63L VAL* 4.2 13.0 - - + -
71L TYR* 3.7 42.2 - - + -
72L SER 3.7 19.5 - - - -
73L LEU* 3.8 22.2 - - + -
80L VAL* 4.9 6.3 - - + -
82L SER* 4.4 13.0 - - - -
94L ILE* 4.2 17.5 - - + -
95L CYS 3.4 11.7 - - - -
96L VAL* 3.8 22.9 - - + -
105L ALA* 4.1 3.2 + - + -
106L GLU* 1.3 74.0 - - - +
108L TRP* 1.3 61.2 + - - +
109L ILE* 4.5 4.3 - - + -
113L PRO* 3.7 3.1 - - - +
114L LEU* 2.9 53.2 + - + +
115L VAL 5.4 1.8 + - - -
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Residues in contact with TRP 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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202K VAL* 4.2 18.4 - - + -
93L HIS* 3.5 2.0 + - - +
94L ILE* 3.4 5.0 - - - -
95L CYS* 2.7 47.1 + - + +
96L VAL* 5.4 0.2 - - - -
97L SER* 5.3 2.2 + - - -
106L GLU* 3.3 40.3 + - + +
107L PHE* 1.3 77.5 + - - +
109L ILE* 1.3 64.4 + - - +
110L ASN 4.1 0.4 - - - -
111L GLY* 3.5 23.3 + - - -
112L THR 3.3 5.4 - - - +
113L PRO* 3.6 41.1 - - + -
164L LEU 6.0 0.4 - - - -
166L PRO* 3.7 40.8 - - + -
169L ILE* 3.6 42.7 - - + +
170L LEU* 4.9 7.0 - - + -
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Residues in contact with ILE 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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71L TYR* 3.7 28.3 - - + -
84L VAL* 4.2 20.9 - - + -
85L ILE 5.7 0.7 - - - +
86L GLU* 4.6 6.5 - - + +
92L VAL* 3.7 18.8 - - + -
93L HIS 3.5 1.1 - - - -
94L ILE* 3.8 26.7 - - + -
107L PHE* 4.5 5.8 - - + -
108L TRP* 1.3 79.9 - - - +
110L ASN* 1.3 73.1 + - - +
111L GLY 3.1 0.4 - - - -
112L THR* 2.8 35.9 + - - -
114L LEU* 3.8 31.9 - - + -
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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