Contacts of the helix formed by residues 2 - 14 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A LEU* 1.3 73.5 - - - +
3A ARG* 1.3 65.3 + - - +
4A ALA* 3.5 11.3 + - - +
5A ASP* 2.9 36.5 + - - +
6A ILE* 3.1 27.9 + - - +
71A PRO* 4.3 4.9 - - - -
2G ASP* 3.7 16.8 - - - +
5G ASP* 4.1 11.1 - - - +
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Residues in contact with ARG 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 ASP* 1.3 75.6 - - - +
4A ALA* 1.3 64.7 + - - +
6A ILE* 3.1 6.9 + - - +
7A LEU* 2.9 40.2 + - + +
71A PRO* 3.8 32.5 - - + +
73A GLN 4.6 5.3 + - - -
74A VAL* 4.0 14.7 - - + +
18E VAL* 4.4 6.7 - - + -
19E ILE* 3.5 29.2 - - - +
21E THR* 3.2 30.2 + - + +
145E HIS* 6.0 0.6 - - - -
149E GLU* 3.4 35.5 + - - +
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Residues in contact with ALA 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP* 3.3 13.6 - - - +
3A ARG* 1.3 77.2 - - - +
5A ASP* 1.3 58.8 + - - +
8A TYR* 2.9 14.4 + - - +
15E ARG* 2.5 48.4 + - + +
18E VAL* 3.8 20.3 - - + +
5G ASP* 4.4 14.4 - - - +
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Residues in contact with ASP 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 3.6 24.2 - - + +
2A ASP* 2.9 33.3 + - - +
4A ALA* 1.3 75.6 - - - +
6A ILE* 1.3 58.8 + - - +
8A TYR* 3.1 8.2 + - - +
9A ASN* 2.8 38.1 + - - +
15E ARG* 5.6 0.7 + - - -
15F ARG* 4.9 5.7 + - - -
2G ASP* 4.2 8.8 - - - +
4G ALA* 4.4 17.4 - - - +
5G ASP* 4.6 7.1 - - - +
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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
----------------------------------------------------------
1A LEU* 4.3 17.7 - - + -
2A ASP 3.1 14.8 + - - +
3A ARG* 3.7 6.1 - - - +
5A ASP* 1.3 75.0 - - - +
7A LEU* 1.3 62.1 + - - +
9A ASN* 3.4 9.1 + - - +
10A ILE* 3.0 29.3 + - + +
65A TRP* 3.3 66.9 - - + +
70A SER* 4.5 3.1 - - - -
71A PRO* 3.9 24.2 - - + -
74A VAL* 4.1 17.7 - - + -
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Residues in contact with LEU 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 ARG* 2.9 30.0 + - + +
4A ALA 4.0 2.7 - - - +
6A ILE* 1.3 77.6 - - - +
8A TYR* 1.3 63.0 + - - +
10A ILE* 3.3 4.8 + - + +
11A ARG* 3.0 28.6 + - - +
74A VAL* 4.2 16.4 - - + -
75A SER 3.5 22.2 - - - +
76A VAL* 3.8 25.4 - - + -
77A PRO* 5.3 0.2 - - + -
15E ARG* 4.3 0.9 - - - +
17E ASP* 3.2 42.8 - - + +
18E VAL* 3.7 15.7 - - + -
19E ILE* 5.1 2.0 - - + +
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Residues in contact with TYR 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 ALA 2.9 20.1 + - - +
5A ASP* 3.4 7.9 - - - +
7A LEU* 1.3 76.8 - - - +
9A ASN* 1.3 73.0 + - - +
11A ARG* 3.4 25.4 + - - +
12A GLN* 3.0 54.3 + - + +
15E ARG* 3.5 15.4 - - - +
12F GLN 3.6 21.4 + - - -
13F THR* 4.3 9.6 - - - -
14F SER 5.5 0.7 + - - -
15F ARG* 4.3 30.9 - - + -
8G TYR* 5.1 16.6 - + - -
11G ARG* 5.4 5.5 + - - -
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Residues in contact with ASN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 4.3 19.6 - - - +
5A ASP* 2.8 29.1 + - - +
6A ILE* 3.8 7.0 - - - +
7A LEU 3.4 0.2 - - - -
8A TYR* 1.3 79.5 - - - +
10A ILE* 1.3 56.0 + - + +
12A GLN 3.4 0.5 + - - -
13A THR* 2.5 41.5 + - - +
65A TRP* 6.4 0.4 - - - +
13F THR* 3.2 37.0 - - + +
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Residues in contact with ILE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.0 33.2 + - + +
7A LEU* 3.6 7.0 - - - +
8A TYR 3.3 0.2 - - - -
9A ASN* 1.3 77.9 - - + +
11A ARG* 1.3 59.3 + - - +
13A THR* 4.3 2.7 - - - -
14A SER* 2.9 37.0 + - - +
63A LEU* 4.0 33.4 - - + +
65A TRP* 4.9 2.2 - - + -
74A VAL* 4.3 5.6 - - + -
76A VAL* 4.0 40.8 - - + -
80A SER* 4.1 5.6 - - - +
81A LEU* 4.1 7.2 - - + -
105A VAL* 4.6 11.0 - - + -
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Residues in contact with ARG 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU 3.0 15.8 + - - +
8A TYR* 3.7 35.5 - - - +
10A ILE* 1.3 78.9 - - - +
12A GLN* 1.3 70.6 + - - +
14A SER* 4.9 3.9 + - - +
80A SER* 4.5 20.6 - - - +
15E ARG* 3.7 23.2 - - - +
17E ASP* 2.7 41.7 + - - -
8G TYR* 4.9 7.7 + - - -
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Residues in contact with GLN 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 TYR* 3.0 51.8 + - + +
9A ASN 3.8 2.5 - - - +
11A ARG* 1.3 88.9 + - - +
13A THR* 1.3 58.3 + - - +
14A SER 3.8 1.9 - - - +
8F TYR* 3.4 18.9 + - - -
12F GLN* 2.8 62.5 + - + +
13F THR* 4.2 4.3 - - + -
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Residues in contact with THR 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASN* 2.5 29.0 + - - +
10A ILE* 4.3 1.0 - - - -
12A GLN* 1.3 75.8 - - - +
14A SER* 1.3 69.1 + - - +
15A ARG* 3.5 13.3 + - - +
62A THR* 5.0 10.1 + - - +
8F TYR* 4.0 9.9 - - + -
9F ASN* 3.4 42.1 - - + +
12F GLN* 3.9 7.9 - - + -
13F THR* 3.6 26.9 - - + -
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Residues in contact with SER 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE 2.9 19.5 + - - +
11A ARG* 4.9 3.1 + - - +
12A GLN 4.7 2.8 - - - +
13A THR* 1.3 84.8 + - - +
15A ARG* 1.3 62.8 + - - +
16A PRO* 3.3 10.7 - - - +
60A ASP* 5.8 1.3 - - - -
62A THR* 4.7 9.4 - - - -
63A LEU* 3.9 25.1 - - - +
80A SER* 2.4 31.8 + - - -
81A LEU* 4.2 4.4 - - - -
82A TRP 5.6 0.9 - - - -
8F TYR* 5.1 1.0 + - - -
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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