Contacts of the helix formed by residues 4 - 15 (chain A) in PDB entry 4H1U
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 LEU 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 4.8 6.0 - - + +
2A GLU* 3.3 17.7 + - + +
3A ALA* 1.3 73.9 - - - +
5A ILE* 1.3 66.5 + - - +
6A PRO 3.4 0.9 - - - -
7A VAL* 3.1 18.8 + - + +
8A ILE* 3.2 18.1 + - + +
294A MET* 5.3 6.0 - - - +
297A ILE* 3.6 18.6 - - + +
298A ARG* 3.6 36.3 - - + +
301A LEU* 4.0 18.6 - - + -
730A ILE* 4.1 34.1 - - + -
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Residues in contact with ILE 5 (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 ALA* 4.8 0.9 - - + +
4A LEU* 1.3 74.6 - - - +
6A PRO* 1.4 72.6 - - + +
7A VAL 3.2 0.3 + - - -
8A ILE* 3.4 2.8 + - - +
9A ASN* 3.0 36.9 + - - +
67A LEU 5.6 1.6 - - - +
141A ASN* 3.4 34.1 - - + +
142A LEU 4.6 9.0 - - - +
143A THR* 4.1 10.3 - - - +
290A ASN* 4.2 4.9 - - - +
293A LEU* 3.8 24.2 - - + -
294A MET* 4.0 28.9 - - + +
297A ILE* 3.8 21.5 - - + -
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Residues in contact with PRO 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.4 31.2 - - + +
5A ILE* 1.4 95.9 - - + +
7A VAL* 1.3 61.1 + - + +
9A ASN* 3.3 13.7 - - + +
10A LYS* 3.1 33.0 + - + +
68A VAL* 6.3 3.4 - - + -
141A ASN* 5.8 7.9 - - - +
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Residues in contact with VAL 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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2A GLU* 5.1 7.2 - - - +
3A ALA 3.8 17.0 - - - +
4A LEU* 3.1 14.3 + - + +
5A ILE 3.1 0.4 - - - -
6A PRO* 1.3 76.6 - - + +
8A ILE* 1.3 71.3 + - + +
10A LYS* 3.1 13.5 + - + +
11A LEU* 3.0 32.4 + - + +
301A LEU* 5.7 1.6 - - + -
726A ILE* 4.1 18.2 - - + +
727A ILE* 4.8 5.6 - - + -
730A ILE* 4.0 35.7 - - + -
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Residues in contact with ILE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.2 10.7 + - + +
5A ILE 4.2 2.9 - - - +
7A VAL* 1.3 83.7 - - + +
9A ASN* 1.3 58.5 + - - +
11A LEU* 3.0 22.3 + - + +
12A GLN* 2.7 53.4 + - + +
25A LEU* 4.7 7.6 - - + -
26A PRO* 3.7 43.1 - - + +
27A GLN* 5.3 0.4 - - + -
143A THR* 6.0 1.3 - - + -
297A ILE* 3.7 34.3 - - + -
301A LEU* 5.2 6.1 - - + -
304A LEU* 4.3 7.6 - - + -
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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
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5A ILE* 3.0 30.0 + - - +
6A PRO* 3.3 13.7 - - + +
8A ILE* 1.3 77.8 - - - +
10A LYS* 1.3 61.2 + - + +
12A GLN* 3.4 8.7 + - - +
13A ASP* 3.2 29.5 + - - +
66A GLN* 3.4 33.7 + - - +
67A LEU 5.5 1.4 + - - -
68A VAL* 4.3 15.4 - - - +
133A LYS* 4.6 6.1 - - - +
143A THR* 2.6 31.2 + - - +
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Residues in contact with LYS 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 PRO* 3.1 20.7 + - + +
7A VAL* 3.1 7.8 + - + +
9A ASN* 1.3 75.4 - - + +
11A LEU* 1.3 60.0 + - - +
13A ASP* 3.3 12.1 + - - +
14A VAL* 3.0 31.4 + - - +
133A LYS* 5.9 1.6 - - - +
726A ILE* 3.7 43.9 - - + +
729A GLU* 5.3 6.7 + - - -
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Residues in contact with LEU 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 VAL* 3.0 19.6 + - + +
8A ILE* 3.0 18.8 + - + +
10A LYS* 1.3 74.9 - - - +
12A GLN* 1.3 65.2 + - - +
14A VAL* 3.3 2.5 + - + +
15A PHE* 3.1 33.8 + - + -
25A LEU* 4.1 19.1 - - + -
301A LEU* 6.1 0.2 - - + -
304A LEU* 4.0 27.8 - - + -
308A ILE* 4.8 2.9 - - + -
723A ALA* 3.8 44.0 - - + +
726A ILE* 4.2 13.5 - - + -
727A ILE* 4.4 16.2 - - + -
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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 ILE* 2.7 28.0 + - + +
9A ASN* 3.5 11.3 - - - +
11A LEU* 1.3 75.7 - - - +
13A ASP* 1.3 61.8 + - - +
15A PHE* 3.6 9.7 + - - +
16A ASN 3.7 5.2 + - - -
20A ALA* 5.6 2.3 - - - +
25A LEU* 4.1 14.8 - - + +
27A GLN* 2.8 37.8 + - - +
64A ILE* 3.6 21.6 - - + +
66A GLN* 2.9 25.5 + - - +
131A HIS* 3.4 14.2 + - - -
143A THR* 3.6 26.0 - - - +
145A VAL* 4.2 3.6 - - - +
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Residues in contact with ASP 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 ASN 3.2 13.4 + - - +
10A LYS* 3.6 10.7 - - - +
11A LEU 3.2 0.2 - - - -
12A GLN* 1.3 74.4 - - - +
14A VAL* 1.3 64.8 + - + +
16A ASN* 3.2 18.5 - - - +
66A GLN* 3.6 8.0 + - - +
94A LEU* 3.8 31.8 - - + +
131A HIS* 3.2 21.8 - - - +
133A LYS* 2.7 32.6 + - - -
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Residues in contact with VAL 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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10A LYS 3.0 19.1 + - - +
11A LEU* 3.3 7.6 + - - +
13A ASP* 1.3 78.8 - - + +
15A PHE* 1.3 69.1 + - + +
16A ASN* 3.2 4.6 + - - +
17A THR 5.2 0.3 + - - -
18A VAL* 4.4 2.4 - - - +
719A ALA* 3.2 46.1 - - + +
722A GLY* 4.6 9.4 - - - -
723A ALA* 4.3 3.1 - - + +
726A ILE* 3.8 21.8 - - + -
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.1 35.4 + - + +
12A GLN 3.8 5.3 - - - +
13A ASP 3.4 0.2 - - - -
14A VAL* 1.3 76.3 - - + +
16A ASN* 1.3 64.7 + - - +
17A THR 3.5 2.0 - - - -
18A VAL* 3.7 24.2 - - + -
19A GLY* 3.8 15.8 + - - +
20A ALA* 3.7 26.0 + - + +
23A ILE* 3.6 47.8 - - + -
25A LEU* 4.5 6.1 - - + -
308A ILE* 4.8 2.7 - - + -
716A MET* 4.1 4.3 - - + -
719A ALA* 4.0 15.7 - - + -
720A LEU* 3.8 16.6 - - + -
723A ALA* 3.6 32.8 - - + -
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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