Contacts of the helix formed by residues 2 - 14 (chain D) in PDB entry 4UM3
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 ASP 2 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D LEU* 1.3 73.5 - - - +
3D ARG* 1.3 65.7 + - - +
4D ALA* 3.5 11.1 + - - +
5D ASP* 2.9 33.9 + - - +
6D ILE* 3.0 28.0 + - - +
71D PRO* 4.3 6.1 - - - -
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Residues in contact with ARG 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 4.7 6.7 - - + -
19C ILE* 3.6 29.0 - - - +
21C THR* 3.4 28.3 + - + +
24C ASP* 5.7 3.8 + - - +
145C HIS* 6.0 0.6 - - - -
146C HIS* 5.9 0.2 - - - -
148C ARG* 6.0 2.0 - - - +
149C GLU* 3.1 38.2 + - - +
2D ASP* 1.3 75.1 - - - +
4D ALA* 1.3 65.0 + - - +
6D ILE* 3.1 6.9 + - - +
7D LEU* 2.8 41.7 + - + +
71D PRO* 3.8 34.6 - - + +
73D GLN 4.6 3.4 + - - -
74D VAL* 4.0 15.6 - - + +
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Residues in contact with ALA 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ARG* 2.8 44.5 + - + +
18C VAL* 4.0 21.3 - - + +
2D ASP* 3.3 13.8 + - - +
3D ARG* 1.3 78.2 - - - +
5D ASP* 1.3 61.7 + - - +
8D TYR* 2.9 16.0 + - - +
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Residues in contact with ASP 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D LEU* 3.6 24.5 - - + +
2D ASP* 2.9 33.7 + - - +
4D ALA* 1.3 80.3 - - - +
6D ILE* 1.3 58.9 + - - +
8D TYR* 3.2 8.2 + - - +
9D ASN* 2.9 37.7 + - - +
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Residues in contact with ILE 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D LEU* 4.2 18.8 - - + -
2D ASP 3.0 16.1 + - - +
3D ARG* 3.6 5.8 - - - +
5D ASP* 1.3 75.1 - - - +
7D LEU* 1.3 57.3 + - - +
9D ASN* 3.3 8.9 + - - +
10D ILE* 2.9 39.5 + - + +
65D TRP* 3.4 67.3 - - + +
70D SER* 4.4 3.8 - - - -
71D PRO* 4.0 23.3 - - + -
74D VAL* 4.1 12.8 - - + -
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Residues in contact with LEU 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ARG* 4.4 0.7 - - - +
17C ASP* 3.4 41.7 - - + +
18C VAL* 3.9 15.0 - - + -
19C ILE* 5.3 1.6 - - + +
3D ARG* 2.8 34.8 + - + +
4D ALA 3.9 2.5 - - - +
6D ILE* 1.3 72.9 - - - +
8D TYR* 1.3 56.7 + - - +
10D ILE* 3.3 4.0 + - + +
11D ARG* 2.9 35.3 + - - +
74D VAL* 4.2 15.9 - - + -
75D SER 3.5 23.1 - - - +
76D VAL* 3.7 24.7 - - + -
77D PRO* 5.3 0.9 - - + -
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Residues in contact with TYR 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ARG* 3.8 12.2 - - - +
4D ALA 2.9 17.3 + - - +
5D ASP* 3.2 8.3 + - - +
7D LEU* 1.3 74.2 - - - +
9D ASN* 1.3 79.2 + - - +
11D ARG* 3.2 26.1 + - - +
12D GLN* 2.9 59.7 + - + +
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Residues in contact with ASN 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D LEU* 4.3 18.8 - - - +
5D ASP* 2.9 27.3 + - - +
6D ILE* 3.6 7.6 - - - +
8D TYR* 1.3 89.0 - - - +
10D ILE* 1.3 62.2 + - + +
12D GLN* 3.3 4.7 + - - +
13D THR* 2.6 40.0 + - + +
65D TRP* 6.4 0.4 - - - +
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Residues in contact with ILE 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 2.9 37.5 + - + +
7D LEU* 3.7 5.8 - - - +
8D TYR 3.2 0.2 - - - -
9D ASN* 1.3 77.6 - - + +
11D ARG* 1.3 60.5 + - - +
13D THR* 4.2 3.1 - - - -
14D SER* 2.9 37.4 + - - +
63D LEU* 4.1 31.6 - - + +
65D TRP* 4.4 9.9 - - + -
74D VAL* 4.3 5.4 - - + -
76D VAL* 4.1 40.4 - - + -
80D SER* 4.4 3.4 - - - +
81D LEU* 4.2 7.0 - - + -
105D VAL* 4.5 10.3 - - + -
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Residues in contact with ARG 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ARG* 3.0 30.7 - - - +
17C ASP* 2.5 38.8 + - - +
7D LEU 2.9 14.8 + - - +
8D TYR* 3.6 28.1 - - - +
10D ILE* 1.3 80.8 - - - +
12D GLN* 1.3 71.5 + - - +
14D SER* 4.7 4.9 + - - +
80D SER* 4.8 19.7 - - - +
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Residues in contact with GLN 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D TYR* 2.9 56.2 + - + +
9D ASN* 3.8 4.9 - - - +
11D ARG* 1.3 90.7 + - - +
13D THR* 1.3 67.0 + - + +
14D SER 4.7 1.8 - - - +
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Residues in contact with THR 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ASN* 2.6 28.1 + - + +
10D ILE* 4.2 1.7 - - - -
12D GLN* 1.3 85.5 - - + +
14D SER* 1.3 69.0 + - - +
15D ARG* 3.5 14.2 + - - +
62D THR* 5.1 9.1 + - - -
63D LEU* 6.1 0.3 - - - +
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Residues in contact with SER 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ILE* 2.9 18.6 + - - +
11D ARG 4.7 4.9 + - - +
12D GLN 4.7 2.3 - - - +
13D THR* 1.3 83.6 + - - +
15D ARG* 1.3 62.8 + - - +
16D PRO* 3.3 10.4 - - - +
60D ASP* 5.9 0.9 - - - -
62D THR* 5.2 6.5 - - - -
63D LEU* 3.7 27.8 - - - -
80D SER 2.3 31.3 + - - -
81D LEU* 4.2 4.2 - - - -
82D TRP 5.6 0.7 - - - -
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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