Contacts of the strand formed by residues 98 - 103 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D MET* 3.3 16.3 + - + +
97D PRO* 1.3 74.4 - - - +
99D VAL* 1.3 74.5 + - - +
100D VAL* 4.5 1.8 - - + -
135D ASP* 3.9 8.3 - - - +
138D ILE* 4.2 17.7 - - + -
139D ARG* 2.9 65.7 + - + +
142D PHE* 3.8 31.4 - - + -
150D THR* 3.5 23.6 - - - +
152D VAL* 4.6 4.7 - - + -
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C ILE* 5.3 5.2 - - + -
97D PRO 6.1 0.2 - - - -
98D LEU* 1.3 77.5 - - - +
100D VAL* 1.3 71.5 + - - +
101D ASP* 3.7 17.0 - - - +
135D ASP* 4.8 1.1 - - - -
149D ASP* 5.8 2.7 - - - +
150D THR 3.1 7.0 + - - +
151D GLN* 3.3 31.8 - - + +
152D VAL 2.9 23.9 + - - +
445D ARG* 4.7 7.4 - - - +
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 4.5 3.8 - - + -
99D VAL* 1.3 80.9 - - - +
101D ASP* 1.3 67.4 + - - +
102D TYR 4.0 2.5 - - - +
131D SER* 3.4 26.8 - - - +
134D ILE* 3.6 29.6 - - + -
135D ASP* 3.8 32.9 + - + +
138D ILE* 4.1 19.7 - - + -
152D VAL* 3.4 17.0 - - + +
154D CYS* 4.9 0.9 - - - -
445D ARG* 3.2 24.7 + - - +
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Residues in contact with ASP 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C VAL* 4.1 20.2 - - + +
99D VAL* 3.7 16.9 - - - +
100D VAL* 1.3 78.4 - - - +
102D TYR* 1.3 62.8 + - - +
103D ARG* 3.8 5.2 + - + +
131D SER* 3.8 1.8 - - - -
151D GLN* 2.9 28.2 + - - +
152D VAL 2.8 10.0 + - - -
153D LEU* 3.4 21.8 - - + +
154D CYS 3.1 23.3 + - - +
445D ARG* 3.7 15.6 + - - +
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Residues in contact with TYR 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 4.5 0.4 - - - +
101D ASP* 1.3 72.4 - - - +
103D ARG* 1.3 72.6 + - - +
104D GLN* 4.7 13.5 + - + -
123D THR* 5.0 1.7 - - - +
126D LYS* 4.6 6.7 + - + -
127D GLU* 3.5 27.2 - - - +
130D THR* 3.4 36.6 - - + -
131D SER* 2.8 28.7 + - - +
134D ILE* 4.0 9.6 - - + -
154D CYS* 3.9 12.6 - - + -
156D LEU* 3.6 22.5 - - + +
165D PRO* 3.4 30.5 - - - +
166D ASP* 3.8 8.9 + - + +
169D ALA* 3.6 30.3 - - + -
445D ARG* 5.3 0.7 + - - -
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Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428C GLU* 3.1 39.6 + - - -
430C PRO* 5.6 5.7 - - - +
440C VAL* 3.2 56.2 + - + +
475C GLU* 5.8 0.8 + - - -
101D ASP* 4.3 10.5 - - + +
102D TYR* 1.3 86.2 - - - +
104D GLN* 1.3 63.1 + - - +
105D LYS* 5.5 0.7 - - - +
123D THR* 5.5 5.6 - - + -
127D GLU* 3.2 11.4 - - - +
153D LEU* 4.6 5.8 - - - +
154D CYS 3.7 21.5 + - - +
155D ASN* 4.9 0.3 - - - -
156D LEU* 3.5 21.5 + - - +
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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