Contacts of the strand formed by residues 121 - 131 (chain L) 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 GLY 121 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117L ASP* 3.6 2.8 - - - +
118L LYS* 3.1 27.6 + - - +
120L SER* 1.3 82.6 + - - +
122L VAL* 1.3 59.6 + - - -
145L PHE* 3.5 19.0 - - - -
146L LEU 3.1 15.3 - - - -
148L GLY 3.4 8.7 - - - -
150L GLY* 3.4 8.7 - - - -
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Residues in contact with VAL 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L VAL* 3.2 27.6 - - + -
116L LEU 2.8 21.8 - - - +
117L ASP* 4.4 0.4 - - - -
121L GLY* 1.3 74.5 - - - -
123L VAL* 1.3 63.6 + - - +
124L ILE* 5.1 4.5 - - + +
145L PHE* 3.1 5.3 - - - -
146L LEU* 2.7 62.3 + - + -
149L SER* 4.7 3.1 - - - +
150L GLY* 3.1 18.1 - - - +
152L PHE* 3.4 19.3 - - + -
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Residues in contact with VAL 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L VAL* 3.1 9.5 - - - +
116L LEU* 2.6 51.3 + - + -
118L LYS* 3.7 35.9 - - + -
122L VAL* 1.3 73.1 - - - +
124L ILE* 1.3 64.0 + - - +
125L ILE* 4.1 21.5 - - + -
143L SER* 4.2 10.5 - - - +
144L LEU 3.4 13.0 - - - +
145L PHE* 3.8 15.7 - - + -
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Residues in contact with ILE 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L PHE* 5.6 10.3 - - + -
87L VAL* 6.0 0.2 - - + -
112L VAL* 3.5 39.5 - - + -
114L ASP 3.6 2.7 - - - -
115L VAL* 4.5 7.4 - - + +
122L VAL* 5.2 5.2 - - + +
123L VAL* 1.3 77.3 - - - +
125L ILE* 1.3 63.9 + - - +
126L MET* 3.6 7.9 + - + +
142L PHE 3.5 3.6 - - - +
144L LEU* 3.0 53.0 + - + +
145L PHE* 4.4 1.6 - - - +
146L LEU* 5.0 19.5 - - + +
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Residues in contact with ILE 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L VAL 3.5 1.7 - - - -
113L ALA* 2.9 34.1 + - + +
114L ASP* 2.9 25.5 + - + +
115L VAL* 6.2 0.4 - - - -
116L LEU* 5.2 7.6 - - + -
123L VAL* 4.2 17.0 - - + -
124L ILE* 1.3 72.7 - - - +
126L MET* 1.3 57.6 + - - +
141L GLN* 3.3 39.7 - - + +
142L PHE 3.7 4.5 - - - +
143L SER* 4.7 9.2 - - - +
158L SER* 4.5 10.3 - - - +
160L LYS 4.5 2.9 - - - +
161L VAL* 3.1 40.8 - - + +
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Residues in contact with MET 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L LEU* 4.0 16.6 - - + -
18L PHE* 6.4 0.9 - - + -
65L GLY 4.6 4.5 - - - +
68L SER* 6.2 3.1 - - - -
69L MET* 3.2 39.7 - - + -
84L PHE* 4.3 7.9 - - + -
110L ALA* 3.9 26.0 - - + -
111L VAL 3.3 10.5 - - - +
112L VAL* 4.4 3.4 - - - +
124L ILE* 3.6 10.7 + - + +
125L ILE* 1.3 73.8 - - - +
127L ASP* 1.3 62.1 + - - +
128L VAL* 3.4 21.3 - - + -
140L ASN 3.7 0.9 - - - +
141L GLN* 3.6 2.2 - - - -
142L PHE* 3.0 61.6 + - + +
144L LEU* 5.4 2.0 - - + -
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Residues in contact with ASP 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L GLU 3.6 0.9 - - - +
110L ALA* 3.2 2.4 - - - -
111L VAL* 2.8 39.9 + - + +
113L ALA* 3.1 23.3 - - + +
125L ILE 4.0 0.8 + - - -
126L MET* 1.3 72.8 - - - +
128L VAL* 1.3 59.3 + - - +
129L TYR* 3.7 22.8 + - + +
139L HIS* 2.6 29.7 + - - +
140L ASN 3.2 2.7 - - - -
141L GLN* 2.8 35.6 + - - +
160L LYS* 4.5 3.3 + - - +
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Residues in contact with VAL 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L PHE* 4.6 5.2 - - + -
65L GLY* 4.1 22.0 - - - +
108L CYS* 4.2 19.3 - - + -
109L GLU 3.2 11.9 - - - +
110L ALA* 4.2 3.8 - - + -
126L MET* 3.4 17.9 - - + -
127L ASP* 1.3 76.2 - - - +
129L TYR* 1.3 65.2 + - - +
130L SER* 4.1 2.4 + - - +
138L CYS 4.0 0.5 - - - +
139L HIS* 3.5 2.0 - - - -
140L ASN* 2.7 48.3 + - + +
142L PHE* 3.3 31.0 - - + -
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Residues in contact with TYR 129 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97L TYR* 4.6 6.7 - - - -
107L LYS 3.4 2.1 - - - +
108L CYS* 3.2 5.9 - - - +
109L GLU* 3.2 36.8 + - + +
111L VAL* 5.7 7.9 - - + -
127L ASP* 3.7 27.9 + - + +
128L VAL* 1.3 74.6 - - - +
130L SER* 1.3 61.1 + - - +
131L TYR* 3.6 28.4 - - + +
136L LEU* 3.7 23.8 - - + -
138L CYS 3.5 2.9 - - - -
139L HIS* 3.6 45.0 + + + -
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Residues in contact with SER 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L ILE* 3.5 22.6 - - - +
65L GLY 4.7 0.2 + - - -
106L LEU* 4.5 8.3 - - - -
107L LYS 3.5 4.5 - - - -
108L CYS* 3.5 12.6 - - - -
128L VAL* 4.5 7.1 + - - +
129L TYR* 1.3 74.2 - - - +
131L TYR* 1.3 55.6 + - - +
136L LEU* 3.6 1.1 - - - +
137L ILE* 2.7 32.8 + - - +
138L CYS* 2.9 40.0 + - - -
140L ASN* 4.6 3.3 + - - -
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Residues in contact with TYR 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L LEU* 2.8 29.6 - - - +
107L LYS* 3.1 28.5 + - + +
109L GLU* 4.2 26.9 + - - -
129L TYR* 3.6 38.3 - - + +
130L SER* 1.3 72.6 - - - +
132L SER* 1.3 60.6 + - - +
133L GLU 4.4 8.5 - - - +
134L LYS* 4.5 9.0 - - - -
135L GLU 2.9 17.3 - - - +
136L LEU* 3.3 41.0 - - + +
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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