Contacts of the helix formed by residues 6 - 21 (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 THR 6 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLU 3.3 1.7 + - - +
5B LEU* 1.3 73.7 - - - +
7B PRO* 1.3 65.7 - - + +
8B GLU* 3.6 13.4 + - - +
9B GLU* 2.8 41.3 + - - +
10B ARG* 2.8 33.0 + - - +
37B ARG* 4.0 13.0 - - - +
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Residues in contact with PRO 7 (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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5B LEU 4.2 2.5 - - - +
6B THR* 1.3 85.6 - - - -
8B GLU* 1.3 63.0 + - - +
10B ARG* 3.3 14.0 - - + +
11B SER* 3.1 25.8 + - - -
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Residues in contact with GLU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 3.2 11.0 + - - +
7B PRO* 1.3 76.3 - - - +
9B GLU* 1.3 66.9 + - - +
11B SER* 3.1 7.2 + - - -
12B GLU* 3.0 46.2 + - + +
129B PHE* 4.2 10.8 - - - -
130B GLU 4.4 3.8 - - - +
131B LYS* 3.4 43.6 - - - +
136B TRP* 4.6 8.7 - - - -
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Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.4 15.9 - - + +
6B THR* 2.8 40.0 + - - +
8B GLU* 1.3 77.6 - - - +
10B ARG* 1.3 65.8 + - - +
12B GLU* 3.1 3.3 + - - +
13B LEU* 2.9 29.7 + - + +
37B ARG* 2.9 36.6 + - - -
129B PHE* 3.6 34.5 - - + -
136B TRP* 3.0 24.9 + - + +
138B VAL* 3.9 8.6 - - - +
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Residues in contact with ARG 10 (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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5B LEU* 3.8 36.5 + - + +
6B THR 2.8 19.3 + - - +
7B PRO* 3.3 17.3 - - - +
9B GLU* 1.3 70.7 - - - +
11B SER* 1.3 62.9 + - - +
13B LEU* 3.3 4.3 + - - +
14B LYS* 3.2 20.6 + - - +
17B ILE* 5.2 14.9 - - - +
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Residues in contact with SER 11 (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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7B PRO 3.1 9.1 + - - -
8B GLU* 3.1 10.0 + - - -
10B ARG* 1.3 76.9 - - - +
12B GLU* 1.3 67.8 + - - +
13B LEU 3.2 0.7 + - - -
14B LYS* 3.3 34.6 + - - +
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 3.0 39.3 + - + +
9B GLU 3.6 7.2 - - - +
11B SER* 1.3 77.8 - - - +
13B LEU* 1.3 63.1 + - + +
14B LYS* 3.7 0.3 + - - +
15B ASN* 4.7 6.4 + - - +
16B SER* 5.3 1.6 + - - -
128B ARG 4.8 5.4 - - - +
129B PHE* 3.5 28.2 - - + -
130B GLU 5.4 1.4 + - - +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.2 12.3 - - + -
9B GLU 2.9 17.9 + - - +
10B ARG* 3.3 5.4 + - - +
11B SER 3.1 0.2 - - - -
12B GLU* 1.3 79.6 - - + +
14B LYS* 1.3 66.1 + - - +
15B ASN 3.2 2.7 - - - -
16B SER* 3.1 6.7 + - - +
17B ILE* 2.9 31.2 + - + +
127B HIS* 3.4 43.5 - - + +
129B PHE* 3.9 15.5 - - + -
138B VAL* 3.7 29.4 - - + -
140B LEU* 4.0 26.0 - - + -
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Residues in contact with LYS 14 (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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10B ARG 3.2 10.2 + - - +
11B SER* 3.3 25.2 + - - +
12B GLU 5.4 0.2 - - - -
13B LEU* 1.3 76.4 - - - +
15B ASN* 1.3 83.8 + - - +
17B ILE* 3.6 7.6 + - - +
18B ALA* 3.0 27.7 + - - +
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Residues in contact with ASN 15 (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 4.7 5.5 + - - +
13B LEU 3.2 0.8 - - - -
14B LYS* 1.3 104.0 - - - +
16B SER* 1.3 61.4 + - - +
18B ALA* 3.3 7.6 + - - +
19B GLU* 2.9 31.8 + - - +
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Residues in contact with SER 16 (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 5.3 1.4 + - - -
13B LEU* 3.1 12.2 + - - +
15B ASN* 1.3 73.3 - - - +
17B ILE* 1.3 58.6 + - - +
19B GLU* 3.1 2.4 + - - -
20B PHE* 2.8 51.8 + - - +
21B HIS* 3.8 2.9 + - - -
103B ARG* 5.9 1.4 + - - -
125B THR* 5.0 1.6 - - - -
127B HIS* 3.2 36.5 + - - -
140B LEU* 4.7 4.5 - - - -
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Residues in contact with ILE 17 (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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5B LEU* 4.8 14.1 - - + -
10B ARG* 5.2 12.8 - - - +
13B LEU* 2.9 29.5 + - + +
14B LYS* 3.8 8.1 - - - +
16B SER* 1.3 75.5 - - - +
18B ALA* 1.3 56.2 + - - +
21B HIS* 3.1 24.1 + - + +
22B THR* 2.6 27.7 + - - +
33B LEU* 3.8 29.8 - - + -
140B LEU* 3.7 23.1 - - + -
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Residues in contact with ALA 18 (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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14B LYS 3.0 15.6 + - - +
15B ASN* 3.4 11.4 - - - +
17B ILE* 1.3 79.9 - - - +
19B GLU* 1.3 61.5 + - - +
22B THR* 3.6 20.3 + - - +
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Residues in contact with GLU 19 (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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15B ASN 2.9 17.7 + - - +
16B SER* 3.8 3.5 - - - +
18B ALA* 1.3 80.2 - - - +
20B PHE* 1.3 81.0 + - + +
22B THR 5.3 0.2 - - - -
103B ARG* 2.7 47.3 + - - -
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Residues in contact with PHE 20 (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* 2.8 31.6 + - - +
19B GLU* 1.3 114.0 - - + +
21B HIS* 1.3 74.3 + - + +
22B THR 3.6 3.2 + - - +
23B TYR* 3.8 9.2 + - - -
98B ILE* 5.2 10.1 - - + -
103B ARG* 3.6 19.1 - - - -
105B VAL* 3.7 39.7 - - + -
123B VAL* 4.1 21.8 - - + +
125B THR* 3.8 13.9 - - + -
142B SER* 3.8 4.9 + - - -
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Residues in contact with HIS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER 3.9 14.1 - - - -
17B ILE* 3.1 22.1 + - - +
20B PHE* 1.3 79.2 + - + +
22B THR* 1.3 58.1 + - - +
23B TYR* 3.7 14.7 - - - -
33B LEU* 3.8 26.4 - - + +
123B VAL* 3.5 28.5 - - + -
125B THR* 2.8 34.9 + - + +
140B LEU* 3.5 40.5 - - + +
142B SER* 2.8 30.9 + - - +
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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