Contacts of the helix formed by residues 7 - 21 (chain B) in PDB entry 4U1D
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 ARG 7 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B PRO* 3.4 3.0 - - - +
6B PHE* 1.3 109.1 - - + +
8B PRO* 1.3 68.0 - - + +
9B GLU* 3.3 33.6 + - - +
10B ASN* 3.4 34.9 + - - +
11B ALA* 3.5 17.8 + - - +
34B PHE* 4.1 5.9 - - - -
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Residues in contact with PRO 8 (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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6B PHE 4.2 3.4 - - - +
7B ARG* 1.3 85.6 - - + +
9B GLU* 1.3 79.1 + - + +
11B ALA* 3.2 12.0 + - + +
12B ILE* 3.2 22.3 + - + +
34B PHE* 3.8 19.7 - - + -
39B ARG* 6.1 0.4 - - - +
47B THR* 3.5 28.7 - - - +
48B VAL* 5.2 3.1 - - + -
50B PRO* 6.3 1.8 - - + -
51B VAL* 3.9 15.4 - - + +
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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
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7B ARG* 3.3 37.2 + - - +
8B PRO* 1.3 93.8 - - + +
10B ASN* 1.3 61.6 + - - +
12B ILE* 3.4 8.4 + - - +
13B LYS* 2.9 45.5 + - - +
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Residues in contact with ASN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 5.8 4.5 - - + -
6B PHE* 4.8 11.3 - - - +
7B ARG* 3.4 48.3 + - - +
8B PRO 3.2 0.6 - - - -
9B GLU* 1.3 78.0 - - - +
11B ALA* 1.3 64.4 + - - +
13B LYS* 3.8 15.7 + - - +
14B ARG* 2.9 27.9 + - - +
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Residues in contact with ALA 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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5B PRO* 5.6 4.7 - - + +
7B ARG 3.5 6.0 + - - +
8B PRO* 3.2 10.4 + - + +
10B ASN* 1.3 78.8 - - - +
12B ILE* 1.3 58.4 + - - +
14B ARG* 3.4 6.0 + - - +
15B ALA* 3.0 27.0 + - - +
30B SER* 5.2 1.7 + - - -
31B LEU* 3.9 15.3 - - + +
34B PHE* 4.0 35.4 - - + -
51B VAL* 4.7 1.6 - - + -
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Residues in contact with ILE 12 (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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8B PRO* 3.2 15.8 + - + +
9B GLU* 3.7 7.9 - - - +
11B ALA* 1.3 74.0 - - - +
13B LYS* 1.3 66.6 + - + +
15B ALA* 3.1 8.8 + - - +
16B ASP* 3.0 28.3 + - - +
31B LEU* 4.5 1.6 - - - -
50B PRO* 4.0 31.9 - - + +
51B VAL* 4.1 22.7 - - + +
54B LYS* 4.0 30.3 - - + -
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Residues in contact with LYS 13 (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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9B GLU* 2.9 31.8 + - - +
10B ASN* 3.8 14.5 + - - +
12B ILE* 1.3 76.1 - - + +
14B ARG* 1.3 58.6 + - - +
16B ASP* 3.0 14.0 + - - +
17B GLU* 2.8 42.0 + - + +
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Residues in contact with ARG 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 ASN 2.9 17.9 + - - +
11B ALA* 3.7 5.6 - - - +
13B LYS* 1.3 75.3 - - - +
15B ALA* 1.3 57.6 + - - +
17B GLU* 2.6 32.1 + - - -
18B LEU* 2.9 46.4 + - + +
30B SER* 5.6 2.7 - - - +
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Residues in contact with ALA 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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11B ALA 3.0 14.6 + - - +
12B ILE* 3.1 11.4 + - - +
14B ARG* 1.3 77.6 - - - +
16B ASP* 1.3 61.2 + - - +
18B LEU* 3.1 4.0 + - - +
19B ILE* 3.0 30.2 + - - +
27B ALA* 4.2 10.3 - - + +
30B SER* 4.7 4.7 + - - +
31B LEU* 4.0 30.5 - - + -
54B LYS* 4.5 4.3 - - - -
58B ILE* 4.5 9.9 - - + -
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Residues in contact with ASP 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 ILE* 3.0 21.5 + - - +
13B LYS* 3.0 11.7 + - - +
15B ALA* 1.3 76.2 - - - +
17B GLU* 1.3 59.3 + - + +
19B ILE* 3.3 10.8 + - - +
20B SER* 2.9 28.4 + - - -
54B LYS* 2.8 31.7 + - - -
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Residues in contact with GLU 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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13B LYS* 2.8 29.2 + - + +
14B ARG* 2.6 46.4 + - - +
16B ASP* 1.3 76.5 - - + +
18B LEU* 1.3 62.2 + - - +
20B SER* 2.8 25.5 + - - -
21B VAL* 3.2 13.6 - - + +
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Residues in contact with LEU 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 ARG* 2.9 38.1 + - + +
15B ALA 3.6 4.3 - - - +
17B GLU* 1.3 76.7 - - - +
19B ILE* 1.3 60.4 + - - +
21B VAL* 3.7 7.0 + - + +
22B GLY 3.5 2.4 + - - -
23B GLU* 2.9 47.2 + - + +
26B ALA* 4.1 15.9 - - + +
27B ALA* 3.6 26.0 - - + -
30B SER* 4.3 11.7 - - - +
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Residues in contact with ILE 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 ALA 3.0 22.7 + - - +
16B ASP* 3.7 15.5 - - - +
17B GLU 3.2 0.2 - - - -
18B LEU* 1.3 73.8 - - - +
20B SER* 1.3 62.0 + - - +
21B VAL 3.1 2.0 - - - -
22B GLY* 2.8 20.4 + - - +
23B GLU 4.5 2.2 - - - +
24B LYS* 3.9 38.0 - - + +
27B ALA* 3.6 13.2 - - + -
54B LYS* 4.9 2.2 - - - +
58B ILE* 3.7 35.0 - - + -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP 2.9 13.3 + - - -
17B GLU* 2.8 19.4 + - - +
19B ILE* 1.3 78.2 - - - +
21B VAL* 1.3 63.2 + - - +
22B GLY* 3.2 1.0 + - - -
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.2 19.0 + - + +
18B LEU* 3.7 10.5 + - + +
19B ILE 3.1 0.4 - - - -
20B SER* 1.3 81.3 - - - +
22B GLY* 1.3 61.4 + - - +
23B GLU* 3.3 14.9 + - + +
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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