Contacts of the strand formed by residues 55 - 60 (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 LYS 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA* 5.9 2.5 - - + -
49B VAL 3.3 5.6 - - - +
50B ASP* 2.4 41.4 + - + +
51B LEU* 5.5 0.2 - - - -
52B GLY 3.6 15.1 + - - -
53B ASN 5.3 2.2 - - - +
54B ARG* 1.3 78.7 - - - +
56B LEU* 1.3 62.0 + - - +
57B GLU* 3.0 30.6 - - - +
75B SER* 3.3 21.3 + - - -
76B GLY 4.8 0.7 + - - -
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Residues in contact with LEU 56 (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 VAL 3.7 1.0 - - - +
48B ALA* 3.3 3.3 - - - -
49B VAL* 2.6 54.3 + - + +
51B LEU* 4.1 13.0 - - + +
54B ARG* 6.0 0.4 - - + -
55B LYS* 1.3 79.6 - - - +
57B GLU* 1.3 61.5 + - - +
58B ILE* 3.7 9.8 + - + -
73B VAL* 4.1 13.5 - - + -
74B GLN 3.7 2.0 - - - +
75B SER* 4.2 9.4 - - - +
167B VAL* 6.3 0.2 - - + -
168B LEU* 4.1 25.4 - - + -
171B ASN* 4.2 14.4 - - - +
203B ASN* 4.4 9.2 - - - +
255B ILE* 3.6 42.6 - - + -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL 3.9 4.0 - - - -
48B ALA* 4.2 12.8 - - + +
55B LYS* 3.0 34.5 - - - +
56B LEU* 1.3 76.7 - - - +
58B ILE* 1.3 61.3 + - - +
59B SER* 5.1 1.5 + - - -
72B VAL* 3.6 2.3 - - - +
73B VAL* 3.5 2.8 - - - -
74B GLN* 2.9 62.9 + - + +
75B SER* 4.3 4.3 - - - -
76B GLY 4.5 4.7 + - - +
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Residues in contact with ILE 58 (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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46B ALA* 3.1 4.9 - - - +
47B VAL* 2.9 41.6 + - + +
49B VAL* 3.8 26.0 - - + -
56B LEU* 4.5 14.8 - - + +
57B GLU* 1.3 77.6 - - - +
59B SER* 1.3 64.0 + - - +
72B VAL 3.5 6.5 - - - +
73B VAL* 4.2 18.8 - - + -
171B ASN* 5.5 1.8 - - + -
175B VAL* 3.6 30.1 - - + -
255B ILE* 4.7 5.4 - - + -
258B GLY 5.6 1.6 - - - -
259B ILE* 4.4 22.2 - - + +
262B LEU* 3.7 20.5 - - + +
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Residues in contact with SER 59 (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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45B SER* 3.2 15.9 - - - -
46B ALA* 4.1 8.7 - - - +
57B GLU 5.1 1.7 + - - -
58B ILE* 1.3 77.7 - - - +
60B SER* 1.3 65.7 + - - +
62B LYS* 6.2 3.4 - - - -
71B ALA* 3.3 5.9 - - - +
72B VAL* 2.8 50.0 + - - +
262B LEU* 4.9 3.1 - - - -
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Residues in contact with SER 60 (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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43B MET 4.8 0.2 - - - -
44B ALA* 3.3 4.3 - - - +
45B SER* 2.9 37.2 + - - +
59B SER* 1.3 79.3 - - - +
61B GLY* 1.3 66.6 + - - +
62B LYS* 3.6 3.9 + - - +
70B SER* 2.8 24.3 + - - -
71B ALA* 4.6 1.8 - - - +
72B VAL* 5.9 1.8 - - - -
179B LEU* 3.5 29.0 - - - +
262B LEU* 5.3 0.4 - - - -
266B THR* 5.6 0.7 - - - -
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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