Contacts of the strand formed by residues 121 - 131 (chain A) in PDB entry 3K3K
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TYR* 4.3 11.8 + - + -
95A ARG* 5.3 2.7 - - - +
97A ASP* 3.4 27.9 + - - +
98A ILE* 4.5 7.9 - - - +
107A GLY 5.9 0.2 - - - -
108A PHE 3.3 7.6 - - - +
109A SER* 3.5 15.7 - - - +
119A ASN 3.6 2.4 + - - +
120A TYR* 1.3 78.0 - - - +
122A SER* 1.3 65.8 + - - +
123A VAL* 4.4 17.4 - - - +
143A TYR* 3.1 4.2 - - - +
144A VAL* 2.9 50.3 + - + +
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Residues in contact with SER 122 (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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23A TYR* 4.3 0.7 - - - -
107A GLY* 3.0 3.7 - - - -
108A PHE* 2.8 55.1 + - - +
120A TYR* 3.8 22.2 - - - -
121A LYS* 1.3 76.7 + - - +
123A VAL* 1.3 69.2 + - - +
124A THR* 4.5 1.4 + - - -
141A GLU* 3.4 23.9 + - - +
142A SER 3.1 14.8 + - - -
143A TYR* 4.0 2.9 - - - +
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Residues in contact with VAL 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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20A PHE* 3.8 25.4 - - + +
21A HIS* 3.2 13.3 - - + -
23A TYR* 3.6 17.5 + - + +
98A ILE* 4.1 20.6 - - + -
105A VAL* 3.8 21.8 - - + -
106A THR 3.4 11.4 - - - +
121A LYS* 4.4 12.6 - - - +
122A SER* 1.3 81.2 + - - +
124A THR* 1.3 67.2 + - - +
125A THR* 4.2 3.1 - - + -
141A GLU* 3.3 2.3 - - - +
142A SER* 2.8 33.2 + - - +
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Residues in contact with THR 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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46A TRP* 4.9 1.0 - - - -
49A VAL* 3.7 24.5 - - + -
58A TYR* 4.7 8.4 + - + +
104A ARG 4.1 0.5 - - - +
105A VAL* 3.5 2.1 - - - -
106A THR* 2.8 48.1 + - - +
107A GLY* 4.7 0.6 - - - -
108A PHE* 6.1 0.3 - - - -
122A SER* 4.5 1.6 + - - -
123A VAL* 1.3 70.6 - - - +
125A THR* 1.3 66.2 + - - +
126A VAL* 4.9 0.2 - - + -
139A VAL* 3.7 27.8 - - + -
140A LEU 3.3 4.3 - - - +
141A GLU* 3.4 29.0 - - + +
168A LEU* 5.6 0.4 - - + -
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Residues in contact with THR 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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20A PHE* 3.8 17.0 - - + -
21A HIS* 2.8 30.2 + - + +
103A ARG 5.6 0.2 - - - -
104A ARG 3.4 7.2 - - - -
105A VAL* 3.6 31.4 - - + -
123A VAL* 4.2 0.7 - - + -
124A THR* 1.3 79.0 - - - +
126A VAL* 1.3 63.5 + - - +
127A HIS* 2.6 32.3 + - - -
139A VAL* 3.5 5.2 - - - +
140A LEU* 2.9 34.3 + - - +
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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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42A PRO* 3.7 28.5 - - + +
45A VAL* 4.1 17.9 - - + -
46A TRP* 4.0 21.1 - - + +
49A VAL* 4.2 16.6 - - + -
103A ARG 4.5 3.5 - - - +
104A ARG* 3.1 36.5 + - + +
125A THR* 1.3 76.8 - - - +
127A HIS* 1.3 69.7 + - - +
137A THR* 3.6 22.7 - - + -
138A VAL 3.8 2.9 - - - -
139A VAL* 4.3 5.8 - - + +
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Residues in contact with HIS 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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13A LEU* 3.4 28.6 - - + +
16A SER* 3.2 34.1 + - - -
20A PHE* 6.0 0.2 - + - -
42A PRO* 4.5 3.8 - - - -
103A ARG 6.2 0.2 - - - -
125A THR* 2.6 40.8 + - - -
126A VAL* 1.3 80.6 + - - +
128A ARG* 1.3 61.0 + - - +
129A PHE* 4.0 10.2 - - + -
137A THR* 3.1 9.9 - - - +
138A VAL 2.9 45.0 + - - +
140A LEU* 3.7 15.0 - - + +
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Residues in contact with ARG 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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12A GLU* 5.6 2.9 - - - +
41A PRO* 6.2 0.2 - - - +
42A PRO* 3.6 29.0 - - + +
43A GLU* 3.5 32.5 + - - -
104A ARG* 4.3 16.6 - - - +
126A VAL 4.5 0.4 + - - -
127A HIS* 1.3 71.8 - - - +
129A PHE* 1.3 81.0 + - - +
130A GLU* 5.1 8.4 + - + +
135A ILE* 4.1 29.8 - - + +
136A TRP 3.8 3.6 - - - -
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Residues in contact with PHE 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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8A GLU* 4.4 2.0 - - + -
9A GLU* 3.7 37.9 - - + -
12A GLU* 3.6 35.2 - - + -
13A LEU* 4.0 9.9 - - + -
127A HIS* 4.0 19.3 - - + -
128A ARG* 1.3 79.1 - - - +
130A GLU* 1.3 60.9 + - - +
135A ILE* 3.2 8.5 - - - +
136A TRP* 2.8 63.5 + + + +
138A VAL* 3.6 38.4 - - + -
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Residues in contact with GLU 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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128A ARG* 5.1 9.5 + - + +
129A PHE* 1.3 76.4 - - - +
131A LYS* 1.3 81.8 + - - +
132A GLU 3.9 10.4 - - - +
133A ASN* 3.4 18.7 - - - +
134A ARG 3.1 7.9 - - - +
135A ILE* 3.7 24.5 - - + +
136A TRP* 4.0 2.9 - - - -
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Residues in contact with LYS 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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130A GLU* 1.3 83.4 - - - +
132A GLU* 1.3 82.3 + - + +
134A ARG* 2.7 39.1 + - + +
136A TRP* 3.6 20.9 - - + -
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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