Contacts of the strand formed by residues 122 - 131 (chain A) in PDB entry 3CS0
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 LYS 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASN* 5.0 8.5 - - - +
114A LYS* 5.2 26.2 - - + +
115A VAL 3.5 4.9 - - - +
116A GLN* 3.2 41.5 + - + +
120A GLY 3.4 6.9 + - - +
121A ARG* 1.3 75.3 - - - +
123A PHE* 1.3 70.0 + - - +
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Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LYS* 3.4 9.4 - - - +
115A VAL* 2.9 36.5 + - + +
117A LEU* 3.7 22.7 - - + -
121A ARG* 3.2 54.3 - - + -
122A LYS* 1.3 80.5 - - - +
124A ASP* 1.3 66.0 + - - +
141A ILE* 3.5 31.6 - - + -
142A GLN 4.1 5.4 - - - +
143A ASN* 3.5 23.3 - - + -
144A PRO* 4.5 0.2 - - + -
145A LYS* 4.1 14.4 - - + -
147A LEU* 4.5 3.4 - - + -
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Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 5.3 7.6 - - - +
113A ILE 3.9 4.2 - - - +
114A LYS* 3.0 44.0 + - - +
123A PHE* 1.3 77.3 - - - +
125A ALA* 1.3 55.6 + - - +
126A LYS* 6.3 2.2 - - + -
141A ILE* 3.6 1.6 - - - -
142A GLN* 2.7 46.5 + - + +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE* 3.0 52.8 + - + +
115A VAL* 3.9 17.5 - - + -
123A PHE 4.1 0.4 + - - -
124A ASP* 1.3 77.2 - - - +
126A LYS* 1.3 68.3 + - - +
139A ILE* 4.2 4.0 - - + -
140A GLN 3.1 21.3 - - - +
141A ILE* 3.9 4.9 - - - +
142A GLN* 4.1 0.4 - - - +
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR 5.9 0.6 + - - -
113A ILE* 5.1 2.0 - - - -
124A ASP* 6.3 2.2 - - + -
125A ALA* 1.3 78.6 - - - +
127A MSE 1.3 62.4 + - - +
139A ILE* 3.4 4.2 - - - -
140A GLN* 2.7 35.2 + - + +
142A GLN* 3.4 30.7 - - + +
426A ASP* 2.9 56.1 + - - +
428A LYS* 3.8 25.3 - - - +
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Residues in contact with MSE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL* 3.9 39.9 - - + +
109A ASN 5.3 1.1 - - - +
110A ALA* 5.4 7.6 - - + +
113A ILE* 5.4 4.6 - - + +
126A LYS* 1.3 80.4 - - - +
128A VAL* 1.3 66.3 + - - +
129A GLY 3.8 24.5 - - - +
130A LYS* 3.4 37.9 - - + +
137A ALA* 4.7 0.9 - - - -
138A LEU 4.1 3.1 - - - -
139A ILE* 4.2 8.3 - - + +
366A SER 5.0 5.8 - - - +
422A ARG* 4.1 32.8 - - + +
426A ASP* 4.3 3.9 + - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 4.5 7.9 - - + -
126A LYS 4.0 0.4 - - - +
127A MSE 1.3 80.1 - - - +
129A GLY* 1.3 64.0 + - - +
138A LEU* 3.0 37.9 + - + +
140A GLN* 3.6 36.3 - - + +
254A MSE 4.2 15.9 - - - +
255A VAL* 4.8 5.2 - - - +
258A GLY* 3.5 21.3 - - - -
419A ALA* 4.9 7.5 - - + +
422A ARG* 3.5 16.0 + - - +
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A MSE 3.8 8.5 - - - +
128A VAL* 1.3 85.8 - - - +
130A LYS* 1.3 65.6 + - - +
137A ALA* 3.6 0.3 - - - -
138A LEU 2.9 21.3 + - - +
254A MSE 3.7 22.0 - - - -
258A GLY 3.7 12.3 - - - -
422A ARG* 4.0 3.1 - - - -
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Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASN* 3.1 30.7 - - - +
107A VAL* 5.4 0.4 - - - -
108A ASP* 3.1 33.4 + - - +
109A ASN* 3.7 5.9 + - - +
127A MSE 3.4 33.8 - - + +
129A GLY* 1.3 75.1 - - - +
131A ASP* 1.3 59.7 + - - +
132A PRO* 3.4 12.2 - - + +
136A ILE 3.7 7.9 - - - -
137A ALA* 3.9 6.7 - - + +
254A MSE 3.8 6.4 - - - +
258A GLY 4.4 4.0 + - - -
259A GLN* 5.6 2.3 - - - +
362A VAL* 5.7 7.8 + - + +
366A SER* 4.0 35.7 + - - +
422A ARG* 4.7 7.8 - - - +
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Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASN* 4.3 2.2 - - - +
130A LYS* 1.3 71.0 - - - +
132A PRO* 1.3 55.9 - - - +
133A ARG* 3.1 11.4 + - - +
134A SER* 2.9 23.0 + - - +
135A ASP 2.8 30.1 + - - -
136A ILE 2.9 16.9 + - - +
250A LEU* 3.3 4.7 - - - +
254A MSE 3.7 19.7 - - + +
260A VAL* 4.1 11.4 - - + +
262A ARG* 3.0 42.4 + - - -
361A GLN* 6.1 0.5 - - - +
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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