Contacts of the helix formed by residues 2 - 18 (chain A) in PDB entry 1K3X
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 GLU 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A PRO* 1.3 73.6 - - - +
3A GLY* 1.3 69.7 + - - +
4A PRO* 3.3 7.0 - - + -
5A GLU* 2.8 14.8 + - - +
6A ILE* 3.0 21.7 + - - +
52A LYS* 3.8 10.5 - - - -
165A GLY 3.7 8.1 - - - +
167A GLY* 2.9 30.0 + - - -
168A ASN 3.1 3.5 + - - -
169A TYR* 2.7 33.4 + - + -
170A LEU* 3.0 23.3 + - + +
427C PED 2.6 37.3 + - - +
428C G 3.5 3.4 - - - +
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Residues in contact with GLY 3 (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 GLU* 1.3 71.8 - - - +
4A PRO* 1.3 63.6 - - - +
6A ILE* 3.2 2.2 + - - +
7A ARG* 2.9 25.8 + - - +
51A GLY* 4.1 15.8 - - - +
52A LYS* 3.8 3.7 - - - +
128A ASP* 6.1 0.4 - - - -
129A VAL* 6.0 0.4 - - - -
130A LEU* 3.8 10.3 - - - +
165A GLY* 2.9 33.6 + - - -
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Residues in contact with PRO 4 (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 GLU 3.4 3.6 - - - -
3A GLY* 1.3 89.5 - - - +
5A GLU* 1.4 64.1 + - - +
7A ARG 3.4 0.2 + - - -
8A ARG* 2.9 35.8 + - - +
129A VAL* 5.8 0.4 - - + -
130A LEU* 4.0 13.0 - - + -
165A GLY 4.2 0.7 - - - +
169A TYR* 3.8 9.0 - - - +
170A LEU* 3.7 18.2 - - + -
205A PRO* 3.5 34.1 - - + +
208A SER* 3.7 9.9 - - - +
209A TYR* 3.7 27.1 - - + +
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PRO* 4.0 17.3 - - + -
2A GLU* 2.8 43.7 + - - +
4A PRO* 1.4 74.8 - - - +
6A ILE* 1.3 62.5 + - - +
8A ARG* 3.4 21.3 + - - +
9A ALA* 2.9 27.7 + - - +
169A TYR* 2.6 27.7 + - - -
208A SER* 3.6 6.8 + - - -
212A ARG* 2.9 29.3 + - - +
554A SO4 4.5 8.1 - - - +
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Residues in contact with ILE 6 (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 PRO* 4.2 21.5 - - + +
2A GLU 3.0 15.9 + - - +
3A GLY 3.9 2.9 - - - +
5A GLU* 1.3 76.5 - - - +
7A ARG* 1.4 59.7 + - - +
9A ALA* 3.3 8.4 + - + +
10A ALA* 2.8 26.7 + - - +
49A THR* 3.9 19.1 - - + -
51A GLY 4.0 13.0 - - - +
52A LYS* 4.0 33.7 - - + +
54A LEU* 4.1 15.6 - - + +
68A ASN* 3.6 29.8 - - + +
74A TRP* 6.3 0.2 - - + -
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Residues in contact with ARG 7 (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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3A GLY 2.9 16.1 + - - +
4A PRO 3.9 0.4 - - - +
6A ILE* 1.4 72.6 - - - +
8A ARG* 1.3 65.7 + - - +
10A ALA* 3.2 18.1 + - - +
11A ASP* 2.9 54.3 + - - +
14A GLU* 3.4 17.8 + - - -
47A VAL 2.9 29.7 + - - -
48A GLU* 3.8 1.0 - - - +
49A THR* 3.0 39.0 + - - +
130A LEU* 3.7 21.8 - - + -
209A TYR* 3.3 28.7 + - + -
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Residues in contact with ARG 8 (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 PRO* 2.9 25.1 + - - +
5A GLU* 3.6 26.3 + - - +
7A ARG* 1.3 77.5 - - - +
9A ALA* 1.3 62.5 + - - +
11A ASP* 3.3 9.5 + - - +
12A ASN* 3.1 27.7 + - - -
208A SER 4.5 3.8 - - - -
209A TYR* 3.8 29.1 - - + +
212A ARG* 3.9 20.4 + - - +
213A GLY* 3.3 31.2 - - - +
551A SO4 2.8 44.8 + - - +
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Residues in contact with ALA 9 (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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5A GLU 2.9 18.1 + - - +
6A ILE* 3.5 12.1 - - + +
8A ARG* 1.3 75.5 - - - +
10A ALA* 1.3 59.5 + - - +
12A ASN* 3.0 11.8 + - - +
13A LEU* 2.9 32.2 + - - +
54A LEU* 4.9 2.2 - - + -
74A TRP* 4.9 23.1 - - + +
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Residues in contact with ALA 10 (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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6A ILE 2.8 17.1 + - - +
7A ARG* 3.2 29.4 + - - +
9A ALA* 1.3 75.8 - - - +
11A ASP* 1.4 63.5 + - - +
13A LEU* 3.1 6.9 + - - +
14A GLU* 2.9 27.5 + - - +
47A VAL* 3.7 15.1 - - + +
49A THR* 3.6 14.6 - - + -
54A LEU* 4.0 9.5 - - + +
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Residues in contact with ASP 11 (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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7A ARG* 2.9 40.7 + - - +
8A ARG* 3.5 9.6 - - - +
9A ALA 3.2 0.2 - - - -
10A ALA* 1.4 76.0 - - - +
12A ASN* 1.3 60.4 + - - +
14A GLU* 3.3 9.8 + - - +
15A ALA* 3.0 28.3 + - - +
209A TYR* 2.5 36.0 + - - -
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Residues in contact with ASN 12 (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 ARG 3.1 16.5 + - - -
9A ALA* 3.0 11.1 + - - +
11A ASP* 1.3 77.6 - - - +
13A LEU* 1.3 65.5 + - + +
15A ALA* 3.4 8.9 + - - +
16A ALA* 3.0 23.9 + - - +
76A VAL* 4.1 16.4 - - + +
551A SO4 2.9 30.1 + - - -
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Residues in contact with LEU 13 (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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9A ALA 2.9 18.7 + - - +
10A ALA* 3.1 6.5 + - - +
12A ASN* 1.3 77.2 - - + +
14A GLU* 1.3 58.7 + - - +
16A ALA* 3.3 2.6 + - - +
17A ILE* 3.0 33.0 + - - +
47A VAL* 4.2 12.8 - - + -
54A LEU* 4.0 23.3 - - + -
56A THR* 5.0 0.9 - - - +
74A TRP* 3.6 60.3 - - + +
75A ARG 5.2 0.2 - - - +
76A VAL* 4.3 9.9 - - + -
100A ILE* 3.8 36.3 - - + -
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Residues in contact with GLU 14 (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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7A ARG* 3.4 22.0 + - - -
10A ALA 2.9 14.2 + - - +
11A ASP* 3.6 11.0 - - - +
13A LEU* 1.3 74.5 - - - +
15A ALA* 1.3 68.2 + - - +
18A LYS* 2.9 54.8 + - + +
44A VAL* 5.9 0.2 - - - -
46A HIS* 3.5 13.6 - - - +
47A VAL* 2.8 41.7 + - + +
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Residues in contact with ALA 15 (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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11A ASP 3.0 17.0 + - - +
12A ASN* 3.8 9.6 - - - +
14A GLU* 1.3 77.4 - - - +
16A ALA* 1.3 61.2 + - - +
20A LYS* 4.5 6.9 + - - -
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Residues in contact with ALA 16 (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 ASN 3.0 17.7 + - - +
13A LEU 3.6 4.3 - - - +
14A GLU 3.1 0.4 - - - -
15A ALA* 1.3 78.6 - - - +
17A ILE* 1.3 63.9 + - + +
20A LYS* 2.7 29.8 + - - -
76A VAL* 3.8 26.7 - - + -
98A LYS* 3.5 15.1 - - + +
100A ILE* 3.9 16.2 - - + -
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Residues in contact with ILE 17 (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 3.0 16.3 + - - +
16A ALA* 1.3 90.4 - - + +
18A LYS* 1.3 70.3 + - - +
19A GLY 3.2 0.9 + - - -
20A LYS* 3.1 23.7 + - - +
22A LEU* 4.3 7.6 - - + -
44A VAL* 3.6 32.7 + - + +
47A VAL* 6.2 0.7 - - + -
93A LEU* 3.9 17.3 - - + +
95A THR* 3.6 23.1 - - + -
98A LYS 3.7 17.5 - - - +
100A ILE* 3.5 36.8 - - + -
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Residues in contact with LYS 18 (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 4.0 0.4 + - - -
14A GLU* 2.9 53.4 + - + +
17A ILE* 1.3 77.9 - - - +
19A GLY* 1.3 63.4 + - - +
20A LYS* 3.3 11.3 + - - +
44A VAL* 3.7 12.1 - - + +
45A THR 3.3 29.8 - - - +
46A HIS* 4.7 3.7 - - - +
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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