Contacts of the strand formed by residues 112 - 117 (chain A) in PDB entry 5DPT
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 LEU 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PRO 3.2 17.7 + - - +
38A VAL* 3.3 10.4 - - + +
39A ILE* 2.7 33.8 + - - +
87A VAL* 3.7 21.8 - - + -
98A MET* 3.8 29.6 - - + +
101A LEU* 4.0 20.2 - - + +
102A TYR* 3.8 30.4 - - + +
105A ASN* 3.6 27.6 - - + +
106A HIS* 4.3 0.9 - - - +
111A PHE* 1.3 72.6 - - - +
113A TYR* 1.3 62.8 + - - +
114A VAL* 4.3 8.5 - - + -
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Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.6 43.7 - + + -
12A TYR* 4.0 6.5 - + + -
13A LYS* 3.6 27.3 - - + +
21A ARG* 3.9 7.3 - - - -
39A ILE* 3.5 29.2 - - + -
86A PHE 3.9 1.7 - - - +
87A VAL* 3.7 24.1 - - - +
88A ASN* 4.4 4.8 + - - +
105A ASN 4.8 2.2 + - - -
107A GLU* 3.7 32.3 + - + +
109A ASP* 2.4 31.6 + - - -
111A PHE* 3.5 29.8 - - + +
112A LEU* 1.3 75.5 - - - +
114A VAL* 1.3 61.8 + - - +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.8 3.5 - - - -
38A VAL* 3.8 19.3 - - + -
39A ILE 2.7 12.8 + - - +
40A VAL* 3.2 14.6 - - + +
41A GLU 3.0 24.3 + - - +
67A PHE* 5.0 4.9 - - + -
85A PHE* 3.5 51.1 - - + -
86A PHE 3.8 2.5 - - - -
87A VAL* 4.0 16.6 - - + -
98A MET* 5.1 2.2 - - + -
101A LEU* 5.0 3.1 - - + -
112A LEU* 4.3 12.6 - - + -
113A TYR* 1.3 77.8 - - - +
115A ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.7 22.8 - - + -
41A GLU 3.2 7.9 - - - +
42A LYS 5.2 0.2 - - - -
43A ALA* 4.8 14.8 - - + +
84A PHE 3.5 0.3 - - - +
85A PHE* 3.2 3.6 - - - -
86A PHE* 2.5 52.5 + - + +
114A VAL* 1.3 75.3 - - - +
116A TYR* 1.3 61.7 + - - +
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Residues in contact with TYR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.8 25.1 - - + -
41A GLU* 3.1 35.8 + - - -
42A LYS* 3.4 15.1 - - + +
43A ALA* 3.0 23.4 + - - -
46A ALA* 4.0 1.9 - - - +
48A VAL* 3.4 23.8 - - + -
49A PRO 3.2 7.0 + - - -
50A ASP* 3.8 0.7 + - - -
51A LEU* 3.1 34.0 + - + +
71A ILE* 5.0 2.7 - - + -
75A ILE* 3.3 22.7 - - + +
83A LEU* 3.5 25.1 - - + -
84A PHE 3.1 9.0 - - - +
85A PHE* 3.8 19.1 - + + -
86A PHE* 4.9 0.4 - - - -
115A ALA* 1.3 76.0 - - - +
117A SER* 1.3 61.4 + - - +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA* 3.8 11.5 - - - +
46A ALA* 3.3 24.0 - - - +
48A VAL* 4.4 3.8 - - - -
83A LEU* 3.3 11.3 - - - +
84A PHE* 2.9 30.0 + - - -
86A PHE* 4.0 9.4 - - - -
116A TYR* 1.3 75.7 - - - +
118A ASP* 1.3 70.8 + - - +
119A GLU* 3.2 24.3 + - - +
121A VAL* 4.6 8.4 - - - +
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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