Contacts of the strand formed by residues 47 - 52 (chain B) in PDB entry 1U31
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 SER 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B ASN* 1.3 79.3 - - - +
48B ILE* 1.3 63.8 + - - +
49B ILE* 6.3 0.7 - - - -
78B LYS* 3.6 20.2 - - - -
120B ASP 3.7 6.5 + - - -
121B THR* 3.4 15.6 - - - +
122B ASP* 2.9 36.9 + - - +
123B LEU 3.0 22.5 + - - -
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Residues in contact with ILE 48 (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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42B ILE* 3.9 33.9 - - + +
45B ALA* 4.0 13.0 - - + -
46B ASN 5.0 0.4 - - - -
47B SER* 1.3 80.3 - - - +
49B ILE* 1.3 73.0 + - - +
50B ILE* 4.3 5.6 - - + -
72B LEU* 4.3 3.8 - - + -
77B LYS* 4.1 19.7 - - + -
78B LYS 2.8 15.7 + - - +
79B VAL* 3.4 19.9 - - + -
80B ARG 3.0 24.9 + - - -
123B LEU* 3.2 17.5 - - + +
125B LEU* 4.0 28.5 - - + -
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Residues in contact with ILE 49 (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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47B SER* 6.3 0.4 - - - -
48B ILE* 1.3 79.6 - - - +
50B ILE* 1.3 67.7 + - - +
51B THR* 4.1 2.2 - - + -
78B LYS 5.6 0.4 - - - +
80B ARG* 3.4 32.1 - - + +
82B GLY* 4.1 17.5 - - - +
114B ILE* 3.5 28.9 - - + -
118B PHE* 3.7 35.2 - - + -
121B THR* 3.5 28.5 - - + +
123B LEU 2.9 6.9 + - - +
124B VAL* 3.2 6.4 - - + +
125B LEU 2.8 25.3 + - - -
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Residues in contact with ILE 50 (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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48B ILE* 4.3 3.4 - - + -
49B ILE* 1.3 76.7 - - - +
51B THR* 1.3 61.1 + - - +
52B PRO* 3.2 14.9 - - + +
56B LEU* 6.2 0.4 - - + -
65B ILE* 3.6 11.0 - - + -
68B LEU* 5.9 0.4 - - + -
69B VAL* 3.6 32.1 - - + -
72B LEU* 6.2 0.9 - - + -
79B VAL* 3.7 15.9 - - + -
80B ARG 2.8 12.0 + - - +
81B PHE* 3.3 28.4 - - + -
82B GLY 2.7 29.3 + - - -
125B LEU* 3.4 31.2 - - + +
127B ILE* 3.7 20.2 - - + -
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Residues in contact with THR 51 (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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49B ILE* 4.1 5.8 - - + -
50B ILE* 1.3 74.3 - - - +
52B PRO* 1.3 62.7 - - - +
82B GLY 3.4 14.6 - - - +
118B PHE* 3.9 14.4 - - + -
124B VAL* 4.1 1.9 - - + +
125B LEU 3.0 7.4 + - - -
126B VAL* 3.5 26.2 - - - +
127B ILE 3.4 11.0 + - - -
129B ALA* 3.2 16.7 - - - +
133B VAL* 3.7 9.9 - - - +
151B LEU* 3.7 19.1 - - + -
153B VAL* 3.6 22.6 - - + +
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Residues in contact with PRO 52 (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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50B ILE* 3.2 18.8 - - + +
51B THR* 1.3 86.7 - - - +
53B GLY* 1.3 58.1 + - - +
56B LEU* 4.1 17.5 - - + -
81B PHE* 4.0 18.4 - - + -
82B GLY 3.5 13.7 - - - +
83B ILE* 4.2 6.6 - - + -
84B HIS 5.4 0.9 + - - -
87B ALA* 3.8 16.8 - - - +
94B LEU* 3.6 27.7 - - + +
98B LEU* 4.1 9.6 - - + -
127B ILE* 3.4 10.1 - - + +
129B ALA* 3.9 4.4 - - - +
132B THR* 5.0 1.2 + - - -
151B LEU* 5.9 1.4 - - - +
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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