Contacts of the strand formed by residues 98 - 103 (chain B) in PDB entry 3U1K
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 LEU 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B MET* 3.2 17.3 + - + -
97B PRO* 1.3 72.8 - - - +
99B VAL* 1.3 71.0 + - - +
100B VAL* 4.8 1.1 - - + -
135B ASP* 3.9 8.9 - - - +
138B ILE* 4.2 11.4 - - + -
139B ARG* 2.9 66.9 + - + +
142B PHE* 3.8 28.0 - - + -
150B THR* 3.4 28.3 - - + +
152B VAL* 4.4 13.7 - - + -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PRO 4.2 0.4 - - - -
98B LEU* 1.3 76.7 - - - +
100B VAL* 1.3 70.2 + - - +
101B ASP* 3.5 21.5 - - - +
135B ASP* 5.0 0.4 - - - -
149B ASP* 6.0 1.3 - - - +
150B THR 3.0 10.1 + - - +
151B GLN* 3.4 30.5 - - + +
152B VAL 2.9 22.5 + - - +
437D ILE* 5.5 3.6 - - + -
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.8 3.4 - - + -
99B VAL* 1.3 79.7 - - - +
101B ASP* 1.3 72.9 + - - +
131B SER* 3.4 35.6 - - - +
134B ILE* 3.7 28.7 - - + -
135B ASP* 3.7 35.4 + - + +
138B ILE* 4.0 20.4 - - + -
152B VAL* 3.4 17.5 - - + +
154B CYS* 4.8 1.3 - - - -
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 3.5 20.6 - - - +
100B VAL* 1.3 80.2 - - - +
102B TYR* 1.3 61.1 + - - +
103B ARG* 3.0 32.1 + - - +
131B SER* 3.8 0.8 + - - -
151B GLN* 3.2 24.1 + - - +
152B VAL 2.8 9.7 + - - -
153B LEU* 3.3 17.8 - - + +
154B CYS* 3.0 26.0 + - - +
445B ARG* 5.5 4.2 + - - -
440D VAL* 3.7 13.7 - - + +
441D THR* 5.8 0.2 - - - +
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 4.5 0.2 - - - +
101B ASP* 1.3 73.4 - - - +
103B ARG* 1.3 70.5 + - - +
104B GLN* 4.1 20.7 - - + +
123B THR* 5.2 0.3 - - - +
126B LYS* 4.1 9.1 + - - -
127B GLU* 3.5 26.5 - - + +
130B THR* 3.6 36.3 - - + -
131B SER* 2.8 27.5 + - - +
134B ILE* 4.0 9.4 - - + -
154B CYS* 3.7 13.7 - - + -
156B LEU* 3.7 21.4 - - + +
165B PRO* 3.2 32.3 - - - +
166B ASP* 3.8 7.3 + - + -
169B ALA* 3.7 30.1 - - + -
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASP* 3.0 49.5 + - - +
102B TYR* 1.3 91.4 + - - +
104B GLN* 1.3 66.2 + - - +
105B LYS* 5.5 0.9 - - - +
122B GLY* 3.6 17.5 - - - +
123B THR* 3.8 20.4 + - - +
127B GLU* 3.5 11.0 - - - +
131B SER* 4.7 1.4 + - - -
154B CYS 3.7 17.0 + - - +
155B ASN* 5.0 0.3 - - - -
156B LEU* 3.5 24.1 + - - +
445B ARG* 4.6 5.3 - - - +
440D VAL* 3.4 33.1 + - - +
441D THR* 3.8 22.4 - - - +
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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