Contacts of the strand formed by residues 150 - 158 (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 THR 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ALA* 5.7 0.2 - - + -
85B VAL 3.2 12.1 - - - +
86B SER* 2.8 21.3 + - - +
96B MET* 5.1 1.9 - - - +
97B PRO 2.9 10.3 + - - +
98B LEU* 3.4 24.8 - - + +
99B VAL* 3.0 26.3 + - - +
142B PHE* 4.3 18.4 - - + -
146B TYR* 3.8 7.3 - - - -
148B TYR 2.5 21.0 + - - -
149B ASP* 1.3 74.2 + - - +
151B GLN* 1.3 66.0 + - - +
152B VAL* 5.0 3.8 - - + -
177B LEU* 5.1 1.6 - - + -
182B ILE* 5.1 4.7 - - + -
437D ILE* 3.6 1.7 - - - +
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Residues in contact with GLN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR* 3.8 0.9 + - - +
84B ALA* 3.4 4.0 - - - -
85B VAL* 2.8 37.4 + - + +
99B VAL* 3.4 20.4 - - + +
101B ASP* 3.2 20.2 + - - -
150B THR* 1.3 74.8 - - - +
152B VAL* 1.3 65.3 + - - +
153B LEU* 3.4 30.4 + - + +
431D PRO* 3.8 8.0 - - - +
436D GLU 4.2 1.4 - - - +
437D ILE* 3.3 24.3 - - + +
438D GLY 2.9 43.5 + - - +
440D VAL* 4.6 1.6 - - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 3.5 29.6 - - + -
83B THR 3.3 3.8 - - - +
84B ALA* 4.4 14.6 - - + -
98B LEU* 4.4 11.4 - - + -
99B VAL 2.9 10.0 + - - +
100B VAL* 3.4 17.2 - - + +
101B ASP 2.8 32.2 + - - +
138B ILE* 3.9 21.8 - - + -
150B THR* 5.0 3.4 - - + -
151B GLN* 1.3 76.6 - - - +
153B LEU* 1.3 57.3 + - - +
154B CYS* 4.7 2.7 - - - -
173B ALA* 3.9 15.5 - - + -
177B LEU* 4.7 8.1 - - + -
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Residues in contact with LEU 153 (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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81B MET 3.9 0.5 - - - +
82B VAL* 3.3 5.4 - - - +
83B THR* 3.0 42.6 + - - +
101B ASP* 3.3 31.0 - - + +
103B ARG* 6.4 0.2 - - - -
151B GLN* 3.4 33.2 - - + +
152B VAL* 1.3 73.0 - - - +
154B CYS* 1.3 62.6 + - - +
155B ASN 4.3 0.2 + - - -
430D PRO* 4.7 0.7 - - + -
431D PRO* 3.5 32.1 - - + -
432D TYR* 3.5 32.9 - - + +
440D VAL* 4.2 10.5 - - + -
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Residues in contact with CYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 4.6 2.9 - - + -
81B MET 3.5 5.8 - - - +
82B VAL* 3.9 24.2 - - + -
100B VAL* 4.8 0.9 - - - -
101B ASP 3.0 17.1 + - - +
102B TYR* 3.7 22.2 - - + -
103B ARG* 3.7 24.0 + - - +
134B ILE* 3.8 28.7 - - - -
152B VAL* 4.7 6.3 - - - -
153B LEU* 1.3 80.0 - - - +
155B ASN* 1.3 59.7 - - - +
156B LEU* 4.2 0.9 - - + -
169B ALA* 4.0 7.0 - - + -
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Residues in contact with ASN 155 (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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80B VAL* 3.6 1.1 - - - -
81B MET* 2.7 57.6 + - + +
103B ARG 5.0 0.2 - - - -
105B LYS* 2.8 26.3 + - - +
154B CYS* 1.3 73.9 - - - +
156B LEU* 1.3 64.0 + - - +
157B LEU* 3.0 16.8 + - - +
394D LEU* 5.1 0.4 - - - +
432D TYR* 3.7 19.2 + - + +
475D GLU* 3.2 28.7 + - - +
477D LEU* 4.4 9.5 - - - +
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Residues in contact with LEU 156 (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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79B ALA 4.0 4.7 - - - -
80B VAL* 4.2 13.9 - - + +
102B TYR* 3.7 38.8 - - + +
103B ARG 3.5 16.1 + - - +
104B GLN* 3.9 29.8 - - + +
105B LYS* 3.2 29.8 + - + +
154B CYS 4.2 0.6 + - - +
155B ASN* 1.3 78.1 + - - +
157B LEU* 1.3 65.4 + - - +
158B ALA* 3.1 3.6 + - - -
159B VAL* 3.9 29.4 - - + -
165B PRO* 4.1 10.5 - - + -
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Residues in contact with LEU 157 (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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63B LEU* 3.6 30.5 - - + -
72B VAL* 4.1 17.5 - - + -
79B ALA* 3.1 11.6 + - + +
81B MET* 4.0 28.0 - - + +
105B LYS* 4.1 7.5 + - - +
155B ASN* 3.0 23.4 + - - +
156B LEU* 1.3 72.0 - - - +
158B ALA* 1.3 63.8 + - - +
377D PHE* 3.7 31.6 - - + -
380D LEU* 3.5 19.6 - - - +
394D LEU* 3.8 24.9 - - + +
396D THR* 5.0 3.6 - - - +
477D LEU* 5.3 1.6 - - + -
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Residues in contact with ALA 158 (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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77B ASP 4.0 6.7 - - - +
78B THR* 3.2 6.1 - - - +
79B ALA 2.8 31.7 + - - +
156B LEU 3.1 3.0 - - - -
157B LEU* 1.3 84.1 - - - +
159B VAL* 1.3 65.2 + - - +
377D PHE* 3.9 27.1 - - + -
379D THR* 4.0 8.5 - - - +
380D LEU* 3.6 21.3 - - + -
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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