Contacts of the strand formed by residues 103 - 109 (chain C) in PDB entry 4B5G
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 103 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU* 3.8 28.3 - - + -
31C ILE* 4.3 11.4 - - + -
75C ARG* 4.8 7.6 - - - +
100C PHE* 3.0 40.7 + - + +
101C GLY 3.4 0.4 - - - -
102C ARG* 1.3 79.2 - - - +
104C SER* 1.3 67.2 + - - +
105C VAL* 4.0 23.6 - - + -
142C ARG* 2.9 13.0 + - - -
143C ASP* 3.5 14.4 - - + +
145C VAL* 4.5 6.5 - - + -
229C LEU* 4.0 24.2 - - + -
256C TYR* 4.5 18.9 + - + -
258C ALA* 5.8 0.9 - - + -
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Residues in contact with SER 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ARG* 2.9 27.2 + - - +
98C CYS 3.4 6.1 - - - -
99C ASP* 2.9 16.1 + - - -
103C LEU* 1.3 80.2 - - - +
105C VAL* 1.3 61.0 + - - +
106C ILE* 4.8 0.3 - - - +
142C ARG* 3.4 14.8 - - - -
143C ASP 2.9 6.9 + - - -
144C ILE* 3.2 24.2 - - - +
145C VAL 2.9 24.4 + - - -
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 4.4 12.6 - - + -
31C ILE* 3.7 36.8 - - + -
33C CYS* 3.6 26.7 - - - -
71C VAL* 4.7 5.0 - - + +
96C VAL 4.0 0.2 - - - +
97C ARG* 3.6 0.3 - - - -
98C CYS* 2.9 35.4 + - - +
100C PHE* 4.4 6.1 - - + -
103C LEU* 4.0 17.9 - - + -
104C SER* 1.3 76.7 - - - +
106C ILE* 1.3 68.0 + - - +
145C VAL* 3.4 13.0 - - + +
147C CYS* 3.9 11.4 - - - -
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Residues in contact with ILE 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C CYS* 4.3 4.0 - - - -
95C PHE* 3.5 35.0 - - + -
96C VAL 3.2 9.9 - - - +
97C ARG* 3.5 27.6 - - + +
104C SER* 4.8 1.6 - - - +
105C VAL* 1.3 81.3 - - - +
107C SER* 1.3 70.1 + - - +
108C LEU* 4.5 1.3 - - + +
137C MET* 3.6 32.3 - - + -
144C ILE* 4.7 4.5 - - + -
145C VAL 2.9 14.6 + - - +
146C VAL* 4.4 20.6 - - + -
147C CYS* 2.9 34.7 + - - +
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C CYS* 3.7 7.2 - - - -
34C VAL 2.9 15.9 + - - -
35C GLN* 2.8 24.3 + - - +
69C VAL* 3.5 10.6 - - - +
70C ALA 3.3 21.4 + - - -
71C VAL* 3.5 14.2 - - - +
95C PHE* 3.5 5.9 - - - -
96C VAL* 2.9 31.9 + - - +
106C ILE* 1.3 73.3 - - - +
108C LEU* 1.3 60.0 + - - +
147C CYS 3.6 2.9 - - - -
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLN* 3.3 5.5 - - - +
69C VAL* 4.3 0.2 - - - -
94C ARG 3.6 4.5 - - - +
95C PHE* 4.0 14.4 - - + -
106C ILE* 4.5 1.8 - - + -
107C SER* 1.3 76.7 + - - +
109C TYR* 1.3 61.7 + - - +
110C LEU* 4.0 27.4 - - + +
126C PHE* 4.1 17.3 - - + -
130C PHE* 3.5 38.6 - - + -
146C VAL* 4.5 8.3 - - + -
147C CYS 2.9 15.0 + - - +
148C GLY* 3.1 3.3 - - - -
149C ASP 2.9 28.0 + - - +
150C TRP* 4.1 30.5 - - + +
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Residues in contact with TYR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ASN* 4.0 4.9 - - - -
35C GLN* 4.1 5.2 - - + -
36C GLU* 3.0 51.2 + - + -
66C TYR* 6.5 0.2 - + - -
67C SER* 3.7 24.7 - - - -
69C VAL* 3.5 20.1 - - + +
94C ARG* 2.9 62.7 + - + +
108C LEU* 1.3 73.5 - - - +
110C LEU* 1.3 66.0 + - - +
111C PRO* 5.6 0.2 - - + -
112C SER 5.9 0.9 - - - -
126C PHE* 5.0 0.4 - - - -
149C ASP* 3.8 29.4 - - + -
151C ASN* 3.9 14.4 - - - -
35Y C 4.5 6.6 + - - -
36Y 3DR 3.1 19.7 + - - -
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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