Contacts of the strand formed by residues 106 - 111 (chain r) in PDB entry 4PJO
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 VAL 106 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44r ILE* 4.0 8.3 - - + -
45r ASN 4.2 2.7 - - - -
47r ARG* 4.7 0.6 - - - +
63r CYS* 4.0 12.3 - - + +
65r MET* 3.6 28.0 - - + -
101r LEU* 4.1 13.5 - - + -
103r GLY* 2.9 19.0 + - - +
104r ASP 3.7 9.0 - - - +
105r SER* 1.3 78.9 - - - +
107r ILE* 1.3 65.3 + - - +
108r VAL 3.6 13.2 - - - +
109r VAL* 3.7 22.4 - - + -
63t LEU* 6.1 0.4 - - + -
65t ARG* 3.8 19.5 - - + +
68t ASN* 3.1 16.1 + - - +
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Residues in contact with ILE 107 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38n TYR* 4.7 13.2 - - + -
45r ASN* 3.0 35.9 + - + +
46r CYS 3.7 20.9 - - - +
47r ARG* 3.7 24.2 - - + +
49r ASN* 6.0 0.2 - - - +
106r VAL* 1.3 75.5 - - - +
108r VAL* 1.3 79.7 + - + +
23t LEU* 4.1 16.8 - - + -
25t TRP* 4.3 13.2 - - + +
27t MET* 4.9 2.7 - - + -
29t TYR* 5.5 0.2 - - - +
64t ILE* 3.9 1.6 - - - +
65t ARG 3.1 23.6 + - - -
68t ASN* 3.2 29.0 + - - +
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Residues in contact with VAL 108 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41n ILE* 4.2 23.1 - - + -
43r LEU 3.8 0.2 - - - +
44r ILE* 3.4 4.5 - - - +
45r ASN* 3.0 32.3 + - + -
106r VAL* 3.6 1.3 - - - +
107r ILE* 1.3 98.1 - - + +
109r VAL* 1.3 70.5 + - - +
110r LEU* 5.0 0.7 - - + -
23t LEU* 4.5 0.4 - - + -
29t TYR* 4.0 28.3 - - + +
62t VAL* 4.0 15.5 - - + -
63t LEU 3.3 9.6 - - - +
64t ILE* 3.9 20.9 - - + -
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Residues in contact with VAL 109 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31r VAL* 4.7 4.6 - - + +
32r LEU* 4.0 19.1 - - + -
42r VAL* 3.5 27.6 - - + -
43r LEU 3.6 2.2 - - - -
44r ILE* 4.2 19.1 - - + +
63r CYS* 5.6 0.9 - - - -
65r MET* 4.5 9.6 - - + -
106r VAL* 3.7 20.4 - - + -
108r VAL* 1.3 80.1 - - - +
110r LEU* 1.3 64.0 + - - +
61t GLU 4.1 0.2 - - - +
62t VAL* 3.4 6.1 - - - +
63t LEU* 2.9 54.2 + - + +
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Residues in contact with LEU 110 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41n ILE* 3.9 27.6 - - + -
45n ILE* 4.8 9.4 - - + -
47n GLU* 4.3 6.7 - - - +
42r VAL* 3.4 5.9 - - - -
43r LEU* 2.9 55.8 + - + +
109r VAL* 1.3 75.9 - - - +
111r ARG* 1.3 78.4 + - - +
112r ASN 3.7 0.3 + - - -
113r PRO* 4.9 2.7 - - + -
59t LEU* 3.8 18.2 - - + +
60t GLY* 3.7 28.5 - - - +
61t GLU 3.4 14.4 - - - +
62t VAL* 3.8 10.3 - - + -
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Residues in contact with ARG 111 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31r VAL* 3.5 20.1 - - + +
34r GLN* 3.0 37.1 + - - +
35r SER* 3.0 27.6 + - - +
38r ASN* 4.1 12.1 - - - +
40r THR* 3.3 34.1 + - - +
42r VAL* 4.1 6.0 - - + +
109r VAL 4.2 0.8 + - - -
110r LEU* 1.3 89.6 - - - +
112r ASN* 1.3 67.5 + - - +
113r PRO* 3.1 5.8 - - - +
61t GLU* 3.2 51.0 + - + +
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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