Contacts of the strand formed by residues 102 - 109 (chain B) in PDB entry 4UM9
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 GLN 102 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B SER* 3.4 33.5 + - - +
64B GLN* 4.1 7.8 - - - +
65B VAL* 3.7 30.0 - - + +
94B LEU* 3.7 10.1 - - + -
96B LEU* 3.5 17.7 - - + -
101B ALA* 1.3 85.9 - - - +
103B THR* 1.3 68.6 + - - +
104B LEU* 4.0 1.8 + - + +
402B VAL 3.7 1.0 - - - +
403B THR* 3.4 1.1 - - - -
404B VAL* 2.8 38.5 + - - +
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Residues in contact with THR 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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65B VAL* 5.4 0.9 - - - +
102B GLN* 1.3 78.6 + - - +
104B LEU* 1.3 65.9 + - - +
105B GLN* 3.9 14.1 + - - +
401B SER* 3.8 29.4 - - - -
402B VAL 3.3 8.1 - - - +
403B THR* 2.9 27.4 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.8 28.9 - - + -
92B LEU* 3.8 24.7 - - + -
94B LEU* 4.3 16.2 - - + -
102B GLN* 4.9 1.3 - - + +
103B THR* 1.3 75.3 - - - +
105B GLN* 1.3 61.7 + - - +
106B VAL* 3.6 13.0 + - + -
400B PHE 3.2 4.0 - - - +
401B SER* 3.3 3.6 - - - -
402B VAL* 2.6 40.9 + - + +
404B VAL* 4.3 7.9 - - + -
418B ILE* 4.5 12.1 - - + -
427B LEU* 5.1 0.9 - - + -
429B LEU* 3.8 38.6 - - + -
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Residues in contact with GLN 105 (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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89B PRO* 3.8 14.0 - - - +
103B THR* 3.9 14.5 + - - +
104B LEU* 1.3 71.8 - - - +
106B VAL* 1.3 59.8 + - - +
107B HIS* 3.6 33.2 + - + +
376B ILE* 4.0 14.8 - - - +
399B SER* 5.1 1.0 - - - -
400B PHE 3.9 5.1 + - - -
401B SER* 2.8 32.5 + - - -
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 4.0 22.2 - - + -
88B ALA 3.6 3.1 - - - +
89B PRO* 4.7 0.7 - - + -
92B LEU* 6.0 0.4 - - + -
104B LEU* 4.3 13.9 - - + +
105B GLN* 1.3 74.8 - - - +
107B HIS* 1.3 62.4 + - - +
108B VAL* 4.3 7.4 - - + -
360B LEU* 4.6 17.7 - - + -
398B ALA 3.8 0.9 - - - +
399B SER* 3.3 3.5 - - - -
400B PHE* 2.7 42.5 + - + +
402B VAL* 4.3 20.4 - - + -
418B ILE* 4.6 9.9 - - + -
427B LEU* 3.8 30.5 - - + -
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Residues in contact with HIS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.8 19.4 - - + +
87B ILE* 3.3 2.9 - - - +
88B ALA* 2.7 54.9 + - + +
89B PRO* 5.2 0.9 - - + -
105B GLN* 3.6 35.5 + - + +
106B VAL* 1.3 73.4 - - - +
108B VAL* 1.3 64.0 + - - +
397B THR* 4.3 5.0 - - + +
398B ALA 3.5 3.1 - - - -
399B SER* 2.6 32.4 + - - +
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Residues in contact with VAL 108 (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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73B LEU* 4.3 0.4 - - - -
86B GLN 3.2 7.9 - - - +
87B ILE* 3.6 24.5 - - + -
106B VAL* 4.3 7.4 - - + -
107B HIS* 1.3 80.3 - - - +
109B ARG* 1.3 62.9 + - - +
358B VAL* 3.4 33.3 - - + +
360B LEU* 4.6 7.4 - - + -
392B MET* 5.1 0.9 - - - +
396B ASP 4.4 0.3 - - - +
397B THR* 3.5 2.4 - - - +
398B ALA* 2.8 45.6 + - + +
400B PHE* 3.5 13.0 - - + -
420B PRO* 3.9 19.1 - - + -
423B LEU* 6.3 0.4 - - + -
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Residues in contact with ARG 109 (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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73B LEU* 3.9 32.8 + - + +
74B SER 3.4 17.7 + - - +
75B VAL* 3.3 37.0 - - - +
85B VAL 4.3 1.5 - - - +
86B GLN* 2.9 34.5 + - - +
108B VAL* 1.3 76.2 - - - +
110B GLN* 1.3 74.2 + - - +
111B THR 3.8 0.2 + - - -
112B GLU* 5.9 0.9 - - - -
358B VAL* 6.2 0.9 - - - -
392B MET* 5.9 0.4 - - - -
395B GLY* 3.3 27.8 + - - +
396B ASP 3.6 11.0 - - - +
397B THR* 2.7 27.3 + - - +
423B LEU* 5.5 0.9 - - - -
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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
------------------------------------------------------------
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