Contacts of the strand formed by residues 93 - 99 (chain L) in PDB entry 5A31
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 93 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92L SER* 1.3 79.3 - - - +
94L ILE* 1.3 64.6 + - - +
95L SER 3.5 0.2 + - - -
110L GLN* 4.6 22.2 - - - +
111L LEU 3.6 4.3 - - - +
112L GLU* 3.4 17.7 - - + +
142L LEU* 3.1 43.9 + - + +
143L ALA* 3.3 27.2 + - + +
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Residues in contact with ILE 94 (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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77L LEU* 6.3 0.4 - - + -
79L ILE* 3.9 33.0 - - + -
91L PRO* 3.9 20.4 - - + -
92L SER 3.7 0.4 - - - -
93L LYS* 1.3 77.6 - - - +
95L SER* 1.3 60.5 + - - +
96L VAL* 4.3 15.0 - - + -
110L GLN* 3.4 4.2 - - - +
111L LEU* 2.8 52.1 + - + +
113L LEU* 3.6 27.3 - - + +
122L VAL* 6.0 2.7 - - + -
139L ILE* 4.3 17.5 - - + -
140L ALA 3.3 9.4 - - - +
141L VAL* 4.2 15.7 - - + -
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Residues in contact with SER 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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93L LYS 3.5 0.2 + - - -
94L ILE* 1.3 75.3 - - - +
96L VAL* 1.3 63.8 + - - +
97L ARG* 3.2 19.9 + - - +
107L GLU* 2.8 32.2 + - - +
110L GLN* 3.9 8.1 - - - -
138L GLN 3.6 1.7 - - - +
139L ILE* 3.6 1.6 - - - -
140L ALA* 2.8 35.1 + - - +
142L LEU* 4.0 25.4 - - - -
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Residues in contact with VAL 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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77L LEU* 4.1 19.3 - - + -
94L ILE* 4.3 15.5 - - + -
95L SER* 1.3 78.5 + - - +
97L ARG* 1.3 64.7 - - - +
98L VAL* 4.2 7.4 - - + -
107L GLU* 3.5 3.6 - - - +
108L ILE* 2.9 46.6 + - + +
109L ARG 3.2 19.2 + - - +
110L GLN* 5.7 0.4 - - - -
111L LEU* 6.2 0.4 - - + -
122L VAL* 4.9 9.9 - - + -
124L LEU* 4.1 17.3 - - + -
137L ILE* 4.2 13.0 - - + -
138L GLN 3.5 7.0 - - - +
139L ILE* 4.4 5.4 - - + -
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Residues in contact with ARG 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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61L PRO* 4.9 5.9 - - - +
63L LEU* 4.7 3.0 - - - +
95L SER* 3.2 18.8 + - - +
96L VAL* 1.3 82.2 - - - +
98L VAL* 1.3 62.4 - - - +
105L LEU* 3.9 19.7 - - + +
106L GLN 3.3 15.9 - - - +
107L GLU* 4.1 12.3 + - + +
137L ILE 3.5 0.3 - - - -
138L GLN* 2.7 74.6 + - - +
140L ALA* 3.8 14.8 - - - +
142L LEU* 3.7 28.5 - - - +
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Residues in contact with VAL 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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96L VAL* 4.2 5.6 - - + -
97L ARG* 1.3 81.7 - - - +
99L GLY* 1.3 59.0 + - - +
104L ASN 4.4 0.2 - - - +
105L LEU* 3.8 4.9 - - - -
106L GLN* 3.1 26.1 + - - +
108L ILE* 3.3 44.9 - - + -
124L LEU* 5.8 0.4 - - + -
132L THR* 4.0 16.2 - - + +
134L THR* 3.7 20.4 - - + +
136L MET 3.2 11.2 - - - +
137L ILE* 4.0 17.0 - - + -
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Residues in contact with GLY 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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98L VAL* 1.3 75.0 - - - +
100L ASN* 1.3 71.6 + - - -
101L ASN 3.4 2.0 - - - -
104L ASN* 3.9 10.3 - - - -
105L LEU* 3.4 12.0 - - - +
134L THR* 3.0 12.9 + - - -
135L PHE 4.0 0.2 + - - -
136L MET* 3.2 28.9 + - - +
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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