Contacts of the strand formed by residues 138 - 145 (chain C) in PDB entry 1S9C
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 CYS 138 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C GLY* 4.4 12.3 - - - -
64C ILE* 4.7 4.7 - - - -
94C LEU* 4.0 3.4 - - + -
95C GLU 3.2 12.6 - - - +
96C LEU* 3.6 18.4 - - + -
97C TYR* 4.0 4.7 - - - -
100C LEU* 4.3 14.8 - - - -
106C LEU* 5.8 0.2 - - - -
128C VAL 4.1 0.3 - - - +
129C TYR* 3.8 0.3 - - - -
130C SER* 3.2 47.5 + - - -
136C LEU* 3.8 6.0 - - - +
137C ILE* 1.3 84.4 - - + +
139C HIS* 1.3 60.8 + - - +
140C ASN* 4.3 13.5 - - - -
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Residues in contact with HIS 139 (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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93C TYR* 3.8 23.6 - + - +
94C LEU* 3.4 4.4 - - - +
95C GLU* 2.9 35.1 + - + +
97C TYR* 3.5 29.5 + - + +
127C ASP* 2.7 31.1 + - - -
128C VAL 3.8 7.6 - - - -
129C TYR* 3.6 34.5 + + + -
138C CYS* 1.3 75.5 - - - +
140C ASN* 1.3 88.7 + - - +
141C GLN* 4.6 4.3 - - + -
162C LYS* 4.5 13.2 - - - -
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Residues in contact with ASN 140 (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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61C GLY 3.0 21.9 + - - -
62C VAL* 3.5 11.5 - - - -
65C GLY* 4.1 13.1 - - - +
92C GLN* 3.2 16.9 + - - +
93C TYR 3.2 3.9 - - - +
94C LEU* 3.3 23.5 - - - +
126C MET 3.7 0.7 - - - +
127C ASP* 3.4 1.7 - - - -
128C VAL* 3.1 36.3 + - + -
130C SER* 4.9 0.8 + - - -
138C CYS* 4.3 8.3 - - - -
139C HIS* 1.3 82.1 - - - +
141C GLN* 1.3 59.8 + - - +
142C PHE* 3.4 26.5 - - + -
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Residues in contact with GLN 141 (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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91C GLU 4.7 0.3 - - - -
92C GLN* 3.8 3.4 - - - -
93C TYR* 2.8 45.0 + - + +
125C ILE* 3.6 21.3 - - + +
126C MET 3.3 5.4 - - - +
127C ASP* 2.9 29.2 + - - +
139C HIS* 4.2 6.0 - - - +
140C ASN* 1.3 72.5 - - - +
142C PHE* 1.3 61.1 + - - +
143C SER* 3.6 5.0 + - - -
160C LYS 2.6 28.2 + - - -
161C VAL* 3.7 8.3 - - - +
162C LYS* 3.1 38.7 + - - +
243C LYS* 4.9 5.0 + - - -
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Residues in contact with PHE 142 (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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62C VAL* 3.9 19.1 - - + -
65C GLY 3.8 4.7 - - - -
66C GLN* 3.8 25.6 - - + -
68C SER* 5.4 0.2 - - - -
69C MET* 3.5 34.1 - - + -
89C HIS* 4.0 6.1 - + - -
91C GLU 4.2 0.2 - - - -
92C GLN* 3.0 31.2 - - - -
124C ILE 3.4 4.0 - - - +
125C ILE 3.7 0.2 - - - -
126C MET* 2.8 50.4 + - + +
128C VAL* 3.4 23.8 - - + -
140C ASN* 3.4 25.8 - - + -
141C GLN* 1.3 71.2 - - - +
143C SER* 1.3 60.3 + - - +
144C LEU* 3.7 16.5 + - + +
217C LEU* 4.7 0.7 - - + -
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Residues in contact with SER 143 (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 GLY* 2.9 26.3 + - - -
91C GLU* 3.2 48.0 + - - +
123C VAL* 4.0 9.0 - - - +
125C ILE* 3.4 26.6 - - - +
141C GLN* 3.6 5.3 + - - -
142C PHE* 1.3 70.1 - - - +
144C LEU* 1.3 63.7 + - - +
161C VAL* 6.3 0.2 - - - -
243C LYS* 5.1 1.3 - - - -
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Residues in contact with LEU 144 (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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69C MET* 3.7 27.6 - - + -
74C LEU* 3.4 32.5 - - + -
84C PHE* 5.7 0.2 - - + -
87C VAL* 4.0 14.8 - - + -
88C LEU 3.4 12.1 - - - +
89C HIS* 4.0 21.1 - - + -
122C VAL 3.5 1.2 - - - +
123C VAL* 3.3 5.3 - - - -
124C ILE* 2.7 55.9 + - + +
126C MET* 4.7 8.3 - - + -
142C PHE* 4.1 13.0 - - + +
143C SER* 1.3 81.5 + - - +
145C PHE* 1.3 60.1 - - - +
146C LEU* 5.6 0.2 - - - -
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Residues in contact with PHE 145 (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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87C VAL* 3.6 2.1 - - - +
88C LEU* 2.6 67.1 + - + +
90C GLY* 4.4 8.5 - - - +
118C LYS* 4.1 17.5 - - + -
120C SER* 4.6 8.5 - - - -
121C GLY* 3.2 46.7 - - - -
122C VAL 3.5 8.5 - - - -
123C VAL* 4.2 13.0 - - + +
143C SER 4.0 1.8 + - - -
144C LEU* 1.3 71.9 - - - +
146C LEU* 1.3 66.7 + - - +
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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