Contacts of the strand formed by residues 122 - 131 (chain H) 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 VAL 122 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115H VAL* 3.2 33.9 - - + -
116H LEU 3.0 22.9 - - - +
117H ASP* 3.9 5.8 - - + +
118H LYS 4.4 0.9 - - - +
121H GLY* 1.3 75.9 - - - +
123H VAL* 1.3 62.5 + - - +
124H ILE* 3.7 7.7 - - + +
144H LEU 3.6 3.1 - - - +
145H PHE* 3.9 3.4 - - - -
146H LEU* 3.6 41.6 + - + +
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Residues in contact with VAL 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H VAL* 3.2 6.3 - - - +
116H LEU* 2.6 49.0 + - + -
118H LYS* 4.0 23.3 - - + -
122H VAL* 1.3 75.6 - - - +
124H ILE* 1.3 65.0 + - - +
125H ILE* 4.2 19.3 - - + -
143H SER* 3.9 21.5 - - - +
144H LEU 3.2 7.2 - - - +
145H PHE* 4.4 14.3 - - + +
161H VAL* 6.1 0.2 - - + -
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Residues in contact with ILE 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H VAL* 5.5 2.9 - - + -
112H VAL* 4.4 17.3 - - + -
114H ASP 3.3 12.3 - - - +
115H VAL* 4.3 10.1 - - + -
122H VAL* 3.7 9.0 - - + +
123H VAL* 1.3 79.8 - - - +
125H ILE* 1.3 60.8 + - - +
126H MET* 3.6 25.7 + - + -
142H PHE 3.3 4.9 - - - +
144H LEU* 2.9 59.5 + - + +
145H PHE* 5.1 1.6 - - - -
146H LEU* 5.9 2.0 - - + -
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Residues in contact with ILE 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H VAL 3.7 1.2 - - - -
113H ALA* 2.9 39.4 + - + -
114H ASP* 2.9 26.5 + - + +
116H LEU* 5.5 3.8 - - + -
123H VAL* 4.2 16.4 - - + -
124H ILE* 1.3 71.6 - - - +
126H MET* 1.3 62.9 + - - +
127H ASP* 4.4 0.9 - - - +
141H GLN* 3.4 37.7 - - + +
142H PHE 3.5 5.2 - - - +
143H SER* 5.1 6.1 - - - +
158H SER* 3.7 18.2 - - - +
160H LYS* 4.5 2.7 - - + +
161H VAL* 3.0 36.3 - - + +
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Residues in contact with MET 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H LEU* 3.5 32.8 - - + -
110H ALA* 3.8 17.0 - - + -
111H VAL 3.7 10.8 - - - +
112H VAL* 4.3 10.8 - - + +
124H ILE* 3.9 24.5 - - + +
125H ILE* 1.3 77.3 - - - +
127H ASP* 1.3 64.8 + - - +
128H VAL* 4.1 2.3 - - + +
140H ASN 3.4 2.9 - - - +
141H GLN* 4.4 0.4 - - - -
142H PHE* 3.0 48.3 + - + +
144H LEU* 4.2 17.3 - - + -
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Residues in contact with ASP 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H GLU 3.7 0.9 - - - +
110H ALA* 3.3 2.1 - - - -
111H VAL* 2.9 38.8 + - + +
113H ALA* 3.4 20.9 - - + +
125H ILE 4.1 0.6 + - - -
126H MET* 1.3 74.5 - - - +
128H VAL* 1.3 61.8 + - - +
129H TYR* 3.6 26.2 + - + -
139H HIS* 2.5 30.1 + - - +
140H ASN 3.2 1.6 - - - -
141H GLN* 3.0 29.7 + - - +
160H LYS* 4.3 5.0 - - - +
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Residues in contact with VAL 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H PHE* 4.2 4.9 - - + -
65H GLY* 3.4 39.5 - - - +
108H CYS* 4.0 19.7 - - + -
109H GLU 3.1 12.1 - - - +
110H ALA* 4.0 10.5 - - + -
126H MET* 4.1 2.7 - - + +
127H ASP* 1.3 78.2 - - - +
129H TYR* 1.3 64.6 + - - +
130H SER* 4.1 1.2 + - - +
138H CYS 3.8 1.2 - - - +
139H HIS* 3.7 2.3 - - - -
140H ASN* 3.1 36.4 + - + +
142H PHE* 3.4 24.0 - - + -
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Residues in contact with TYR 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H TYR* 5.0 2.9 - - - -
107H LYS 3.6 1.6 - - - +
108H CYS* 3.3 3.2 - - - -
109H GLU* 3.0 37.1 + - + +
111H VAL* 5.6 7.0 - - + -
127H ASP* 3.6 28.4 + - + +
128H VAL* 1.3 74.2 - - - +
130H SER* 1.3 61.7 + - - +
131H TYR* 3.5 29.8 - - + +
136H LEU* 3.6 27.4 - - + -
138H CYS 3.5 2.7 - - - -
139H HIS* 3.7 42.5 + + + -
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Residues in contact with SER 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H ILE* 3.4 26.9 - - - +
65H GLY* 4.5 1.7 + - - -
106H LEU* 4.5 10.3 - - - -
107H LYS 3.3 5.4 - - - -
108H CYS* 3.5 14.0 - - - +
128H VAL* 4.4 6.1 + - - +
129H TYR* 1.3 76.3 - - - +
131H TYR* 1.3 54.8 + - - +
136H LEU* 3.8 0.7 - - - +
137H ILE* 2.7 37.2 + - - +
138H CYS* 3.1 29.4 + - - -
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Residues in contact with TYR 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H LEU* 3.4 11.0 - - - +
107H LYS* 3.1 38.3 + - + +
109H GLU* 3.9 30.0 + - - -
129H TYR* 3.5 41.6 - - + +
130H SER* 1.3 75.0 - - - +
132H SER* 1.3 64.0 + - - +
135H GLU 3.3 16.6 - - - +
136H LEU* 3.3 39.6 - - + +
137H ILE* 4.5 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