Contacts of the strand formed by residues 104 - 107 (chain L) in PDB entry 5OOM
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 ASN 104 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39L ARG* 3.3 14.8 - - - -
41L VAL* 3.8 16.2 - - + -
86L ILE* 4.1 0.3 - - - +
87L VAL* 2.9 42.0 + - + +
88L GLY 3.3 6.5 + - - +
100L PHE* 3.3 41.6 - - - +
102L SER* 2.4 26.8 + - - -
103L ASN* 1.3 71.3 - - - +
105L VAL* 1.3 62.8 + - - +
121L THR* 4.3 7.4 + - - +
122L PRO 5.0 0.6 + - - -
158Q GLN* 3.3 17.0 - - - +
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Residues in contact with VAL 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L ILE* 4.9 3.4 - - + -
38L VAL* 3.6 35.2 - - + -
39L ARG 3.3 5.7 + - - -
40L VAL* 3.4 10.4 - - + +
41L VAL* 3.0 22.9 + - - +
73L ILE* 4.5 7.0 - - + -
75L LEU* 4.1 8.3 - - + -
84L ALA* 3.6 29.6 - - + -
85L LEU 3.4 10.5 - - - +
86L ILE* 4.0 20.2 - - + -
87L VAL* 4.4 0.6 - - - +
103L ASN 3.8 5.2 - - - +
104L ASN* 1.3 80.6 - - - +
106L VAL* 1.3 65.7 + - - +
107L LEU 4.8 0.2 - - - +
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Residues in contact with VAL 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L VAL* 3.6 16.8 - - + +
42L ASP* 3.3 18.2 - - - +
84L ALA* 3.5 0.5 - - - -
85L LEU* 2.9 38.9 + - + +
87L VAL* 3.7 24.0 - - + -
105L VAL* 1.3 76.2 - - - +
107L LEU* 1.3 75.7 + - - +
114L PRO* 4.8 9.2 - - + -
116L GLY* 5.9 0.2 - - - -
119L ILE* 3.7 30.3 - - + -
137L VAL* 4.4 13.0 - - + -
140L ILE* 6.1 0.4 - - + -
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Residues in contact with LEU 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L VAL* 4.1 13.5 - - + -
42L ASP* 2.7 22.8 + - - +
44L SER* 4.1 13.2 - - - -
46L LEU* 4.0 23.3 - - + -
47L GLY 4.4 1.1 - - - +
75L LEU* 3.7 29.4 - - + -
77L ILE* 3.7 21.5 - - + -
82L LYS* 3.7 22.4 - - + -
83L LYS 4.0 4.5 - - - +
84L ALA* 4.3 1.1 - - + -
105L VAL* 4.1 0.4 + - + -
106L VAL* 1.3 87.7 - - - +
108L ILE* 1.3 61.5 + - - +
114L PRO* 3.6 12.5 - - - +
115L VAL* 3.7 18.7 + - + -
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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