Contacts of the strand formed by residues 100 - 110 (chain C) in PDB entry 4A8X
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 GLY 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C MET* 3.6 19.0 - - - -
95C ASP* 3.3 25.8 + - - +
98C ARG* 2.7 21.6 + - - +
99C PRO* 1.3 74.2 - - - +
101C TYR* 1.3 64.7 + - - -
102C ARG* 3.8 3.6 + - - +
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Residues in contact with TYR 101 (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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170A ARG* 5.8 2.4 - - - -
200A HIS* 2.7 33.0 + + - -
201A LEU* 4.2 6.6 - - + +
43C MET* 3.5 34.6 - - + +
46C PHE* 3.0 40.1 + - + -
47C SER* 4.5 4.5 - - - -
48C ARG 4.5 2.2 - - - -
49C GLY 4.5 0.3 + - - -
92C VAL* 4.3 13.0 - - + -
93C PHE* 3.5 7.9 - - - -
94C MET* 3.6 44.9 - - + -
98C ARG* 4.7 5.4 + - - -
100C GLY* 1.3 75.1 - - - -
102C ARG* 1.3 63.2 + - - +
132C TYR* 3.6 30.7 + + - -
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Residues in contact with ARG 102 (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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43C MET* 3.6 6.7 - - - -
92C VAL* 3.3 5.4 - - - +
93C PHE* 3.0 61.5 + - + +
95C ASP* 2.8 43.3 + - + -
98C ARG* 4.3 19.7 - - - +
100C GLY 4.0 7.6 - - - +
101C TYR* 1.3 81.0 - - - +
103C VAL* 1.3 65.3 + - - +
104C LYS* 6.1 2.0 - - - +
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Residues in contact with VAL 103 (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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40C HIS* 4.9 15.5 - - + -
41C HIS 5.3 1.8 - - - +
43C MET* 3.4 31.2 - - + +
90C ALA* 3.6 26.7 - - + -
91C ILE 3.4 5.6 - - - +
92C VAL* 4.1 9.4 - - + -
93C PHE* 4.4 1.1 - - - -
102C ARG* 1.3 77.2 + - - +
104C LYS* 1.3 65.3 - - - +
105C GLU* 4.8 3.7 - - + +
134C ASP* 5.4 0.4 - - + -
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Residues in contact with LYS 104 (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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90C ALA* 3.3 2.2 - - - -
91C ILE* 2.9 34.8 + - + +
93C PHE* 3.8 21.1 - - + -
102C ARG* 6.1 2.0 - - - +
103C VAL* 1.3 74.7 - - - +
105C GLU* 1.3 74.8 + - - +
106C ILE* 3.5 12.0 + - + +
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Residues in contact with GLU 105 (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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40C HIS* 3.4 23.9 - - + +
88C ASN* 3.3 29.9 + - - +
89C PHE 3.6 5.6 - - - -
90C ALA* 3.9 3.1 - - + -
103C VAL* 5.3 4.0 - - + +
104C LYS* 1.3 81.7 - - - +
106C ILE* 1.3 58.9 + - - +
107C GLY 5.2 1.1 - - - +
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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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66C LEU* 4.0 24.0 - - + -
89C PHE* 2.8 32.6 + - + +
90C ALA* 4.3 1.8 - - - +
91C ILE* 3.7 34.1 - - + -
104C LYS* 3.5 15.0 + - + +
105C GLU* 1.3 77.1 - - - +
107C GLY* 1.3 56.9 + - - +
117C ASP* 4.5 0.5 - - - +
120C MET* 3.3 23.5 - - + +
121C THR 5.8 0.9 - - - +
122C LEU* 5.4 6.3 - - + -
125C GLN* 3.8 35.6 - - + +
133C LEU* 4.7 6.7 - - + -
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Residues in contact with GLY 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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66C LEU* 3.9 11.7 - - - -
88C ASN* 3.7 5.4 + - - +
89C PHE* 2.8 27.4 + - - +
105C GLU* 4.0 1.2 - - - +
106C ILE* 1.3 83.2 - - - +
108C SER* 1.3 62.6 + - - -
117C ASP* 3.4 16.2 - - - -
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Residues in contact with SER 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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66C LEU* 4.7 0.9 - - - -
86C HIS* 3.2 32.6 + - - -
87C PHE 3.0 14.8 - - - -
88C ASN* 3.7 6.1 - - - -
89C PHE* 4.5 0.9 - - - -
107C GLY* 1.3 75.6 - - - -
109C THR* 1.3 70.5 - - - +
115C GLY* 5.8 1.7 - - - -
117C ASP* 3.3 25.2 + - - +
118C ASP* 4.6 1.2 - - - +
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Residues in contact with THR 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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66C LEU* 3.8 28.9 - - + -
67C LYS* 4.3 4.3 - - - +
70C THR* 2.8 31.4 + - - +
86C HIS* 3.5 7.6 - - - -
87C PHE* 2.8 43.8 + - - +
89C PHE* 3.8 1.7 - - + -
108C SER* 1.3 81.0 - - - +
110C MET* 1.3 64.1 + - - +
115C GLY* 6.3 0.9 - - - -
118C ASP* 3.7 23.1 - - - +
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Residues in contact with MET 110 (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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70C THR* 6.0 0.9 - - - -
84C GLY* 3.7 21.1 - - - +
85C THR 3.1 14.4 - - - +
86C HIS* 3.8 31.6 - - + -
87C PHE* 4.6 1.8 - - - -
109C THR* 1.3 77.7 - - - +
111C SER* 1.3 75.9 + - - +
112C GLY 3.2 0.7 + - - -
113C ARG* 3.1 47.5 + - + +
118C ASP* 5.3 0.2 + - - -
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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