Contacts of the strand formed by residues 123 - 131 (chain A) in PDB entry 3K5N
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 PRO 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLY 3.6 7.0 - - - +
6A PHE* 3.7 9.2 - - + -
120A ILE* 3.9 3.5 - - - +
121A THR* 3.3 10.1 - - - +
122A SER* 1.3 91.0 - - - +
124A VAL* 1.3 71.0 + - - +
142A PRO* 3.6 5.0 - - - +
143A HIS* 3.1 40.3 + - + +
144A PRO 5.5 0.2 - - - +
146A TYR* 4.0 11.2 - - + +
147A ARG* 3.2 26.2 - - - +
357A THR* 3.9 13.2 - - + +
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Residues in contact with VAL 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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4A ALA* 3.2 5.9 - - - -
5A GLY 3.0 33.8 + - - +
7A ILE* 3.7 22.4 - - + -
25A LEU* 3.8 29.6 - - + -
120A ILE* 3.5 28.9 - - + -
122A SER 3.8 0.2 - - - +
123A PRO* 1.3 83.7 - - - +
125A TRP* 1.3 70.2 + - - +
126A VAL* 5.2 0.2 - - + -
140A LEU* 4.5 10.1 - - + -
141A LYS 3.2 11.4 - - - +
143A HIS* 3.4 12.1 + - - +
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Residues in contact with TRP 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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2A ALA* 4.4 16.4 - - + -
3A GLN* 3.4 15.0 - - - -
4A ALA* 3.8 24.2 - - + -
124A VAL* 1.3 76.4 - - - +
126A VAL* 1.3 60.6 + - - +
127A GLU* 6.4 0.7 - - + -
139A ARG 3.6 1.1 - - - +
140A LEU* 3.4 6.2 - - - -
141A LYS* 2.8 49.2 + - + +
142A PRO 3.4 24.7 + - - -
143A HIS* 3.3 36.0 + + - +
144A PRO* 4.4 6.6 - - + +
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Residues in contact with VAL 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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1A MET 3.2 4.9 - - - +
2A ALA* 3.0 6.2 - - - -
3A GLN* 2.8 50.9 + - + +
4A ALA 5.3 0.7 - - - -
25A LEU* 4.3 21.1 - - + -
32A LEU* 4.6 5.8 - - + -
34A VAL* 4.1 11.0 - - + -
124A VAL* 5.2 0.4 - - + -
125A TRP* 1.3 76.3 - - - +
127A GLU* 1.3 75.6 + - - +
135A ILE* 3.7 28.7 - - + -
138A ALA* 4.1 8.3 - - + -
139A ARG 3.5 5.2 - - - +
140A LEU* 5.0 6.7 - - + -
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Residues in contact with GLU 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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1A MET 4.2 10.1 + - - +
2A ALA* 4.0 23.7 + - + +
125A TRP* 4.2 0.8 - - + -
126A VAL* 1.3 78.4 - - - +
128A GLY* 1.3 59.8 + - - +
138A ALA* 3.1 3.5 - - - -
139A ARG* 2.1 80.8 + - - +
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Residues in contact with GLY 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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1A MET* 3.4 27.9 + - - +
126A VAL 4.2 0.4 + - - -
127A GLU* 1.3 78.4 - - - +
129A ASP* 1.3 63.4 + - - +
130A MET 4.0 0.2 - - - -
135A ILE* 3.3 17.0 - - - +
136A VAL 3.5 7.4 - - - -
137A ASN 4.0 3.8 - - - -
138A ALA* 4.0 2.0 - - - -
139A ARG* 4.9 2.8 - - - +
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Residues in contact with ASP 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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128A GLY* 1.3 75.0 - - - +
130A MET* 1.3 64.8 + - - +
131A HIS* 3.3 5.8 + - + +
135A ILE* 4.1 1.3 - - - -
136A VAL* 2.7 49.1 + - + +
137A ASN* 4.4 15.7 + - + +
190B SER* 5.6 1.4 + - - -
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Residues in contact with MET 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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1A MET* 3.4 41.5 - - + -
3A GLN* 5.3 0.4 - - - +
32A LEU* 4.2 12.6 - - + -
128A GLY 4.0 1.4 - - - -
129A ASP* 1.3 73.5 + - - +
131A HIS* 1.3 58.6 + - - +
133A GLY* 3.6 38.6 - - - +
134A THR 3.4 7.0 - - - +
135A ILE* 3.6 20.0 - - + +
190B SER* 3.0 46.0 + - - +
191B LEU 3.8 13.0 - - - +
192B ASP* 4.2 12.3 - - + -
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Residues in contact with HIS 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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129A ASP* 3.3 8.1 + - + +
130A MET* 1.3 74.9 - - - +
132A ASN* 1.3 90.6 + - - +
133A GLY 3.4 0.9 - - - -
134A THR* 2.7 24.4 + - - +
136A VAL* 4.6 13.7 - - + +
189B SER* 3.4 28.2 + - - -
190B SER* 5.2 1.1 - - - -
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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