Contacts of the strand formed by residues 121 - 131 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TYR* 4.8 2.3 + - + -
95B ARG* 5.5 1.6 - - - +
97B ASP* 3.4 29.8 + - - +
98B ILE* 4.7 6.5 - - - +
108B PHE 3.4 4.9 - - - +
109B SER* 3.6 14.1 - - - +
119B ASN 4.2 4.7 - - - +
120B TYR* 1.3 78.2 - - - +
122B SER* 1.3 63.1 + - - +
123B VAL* 4.0 21.5 - - + +
143B TYR* 3.2 2.9 - - - +
144B VAL* 2.9 49.6 + - + +
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASP* 5.0 0.2 - - - +
107B GLY* 3.0 4.3 - - - -
108B PHE* 2.9 49.9 + - - +
120B TYR* 3.7 23.8 + - - -
121B LYS* 1.3 74.0 - - - +
123B VAL* 1.3 69.6 + - - +
124B THR* 4.5 1.6 + - - -
141B GLU* 3.2 26.9 + - - +
142B SER 3.2 12.1 + - - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 4.1 37.2 - - + +
21B HIS* 3.5 8.0 - - + -
23B TYR* 4.5 6.9 + - + +
98B ILE* 4.2 14.4 - - + -
105B VAL* 4.0 19.7 - - + -
106B THR 3.5 10.5 - - - +
107B GLY* 4.1 0.4 - - - -
121B LYS* 4.0 23.1 - - + +
122B SER* 1.3 79.4 + - - +
124B THR* 1.3 65.1 + - - +
125B THR* 4.3 0.7 - - + -
141B GLU* 3.3 3.3 - - - +
142B SER* 2.9 35.7 + - - +
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TRP* 4.9 0.9 - - - -
49B VAL* 3.9 23.3 - - + -
104B ARG 4.1 0.3 - - - +
105B VAL* 3.5 2.3 - - - -
106B THR* 2.9 47.6 + - - +
107B GLY* 5.9 0.3 - - - -
108B PHE* 6.2 0.2 - - - -
122B SER* 4.5 2.3 + - - -
123B VAL* 1.3 73.3 - - - +
125B THR* 1.3 69.6 + - - +
126B VAL* 4.8 0.2 - - + -
139B VAL* 3.6 27.6 - - + -
140B LEU 3.2 5.4 - - - +
141B GLU* 3.5 25.0 + - + +
168B LEU* 5.6 0.4 - - + -
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER* 5.7 0.2 - - - -
20B PHE* 3.8 18.4 - - + -
21B HIS* 2.8 31.8 + - + +
103B ARG 5.7 0.9 - - - -
104B ARG 3.5 6.1 - - - -
105B VAL* 3.8 28.5 - - + -
123B VAL* 4.3 0.9 - - + -
124B THR* 1.3 80.8 - - - +
126B VAL* 1.3 63.8 + - - +
127B HIS* 2.7 31.3 + - - -
139B VAL* 3.4 5.4 - - - +
140B LEU* 2.8 33.9 + - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PRO* 3.8 23.8 - - + +
45B VAL* 4.2 15.0 - - + -
46B TRP* 3.9 23.6 - - + +
49B VAL* 4.3 15.0 - - + -
103B ARG 4.3 4.3 - - - +
104B ARG* 3.1 37.2 + - + +
124B THR* 4.8 1.3 - - + -
125B THR* 1.3 77.4 - - - +
127B HIS* 1.3 71.6 + - - +
137B THR* 3.6 22.2 - - + -
138B VAL 3.8 2.5 - - - -
139B VAL* 4.5 6.7 - - + +
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Residues in contact with HIS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.4 29.4 - - + +
16B SER* 3.2 35.2 + - - -
42B PRO* 4.6 3.1 - - - -
125B THR* 2.7 36.2 + - - -
126B VAL* 1.3 81.3 + - - +
128B ARG* 1.3 61.5 + - - +
129B PHE* 4.2 10.1 - - + -
137B THR* 3.2 11.9 - - - +
138B VAL 2.9 44.2 + - - +
140B LEU* 3.8 14.6 - - + +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLU* 4.8 5.2 - - - +
42B PRO* 3.6 26.0 - - + +
43B GLU* 2.7 39.2 + - - -
104B ARG* 3.5 26.1 - - - +
127B HIS* 1.3 73.3 - - - +
129B PHE* 1.3 76.7 + - - +
130B GLU* 3.5 28.5 + - - +
135B ILE* 4.3 15.6 - - + +
136B TRP 3.8 2.7 - - - -
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 4.2 5.8 - - - -
9B GLU* 3.6 39.9 - - + -
12B GLU* 3.5 39.3 - - + -
13B LEU* 3.9 26.5 - - + -
127B HIS* 4.2 8.3 - - + -
128B ARG* 1.3 77.5 - - - +
130B GLU* 1.3 70.1 + - - +
135B ILE* 3.3 2.1 - - - +
136B TRP* 2.8 63.1 + + + +
138B VAL* 3.5 38.4 - - + -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 4.4 4.9 - - - +
12B GLU* 5.4 1.4 - - - +
128B ARG* 3.5 30.5 + - + +
129B PHE* 1.3 81.4 - - - +
131B LYS* 1.3 70.2 + - - +
132B GLU 5.3 4.3 - - - +
134B ARG 3.2 12.1 - - - +
135B ILE* 4.1 19.1 - - + +
136B TRP* 4.0 2.2 - - - -
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 3.4 37.6 - - - +
130B GLU* 1.3 77.2 - - - +
132B GLU* 1.3 86.4 + - + +
134B ARG* 3.1 23.9 + - - +
136B TRP* 3.5 20.2 - - + -
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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