Contacts of the helix formed by residues 7 - 27 (chain B) in PDB entry 1HUL
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 THR 7 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE 3.2 7.1 + - - +
6B PRO* 1.3 68.8 - - - +
8B SER* 1.3 72.9 + - - +
10B LEU* 2.9 15.6 + - + +
11B VAL* 2.8 29.3 + - - +
74B LEU 5.7 3.6 - - - +
75B ILE* 6.0 3.5 - - + +
78B TYR* 5.1 26.4 - - + -
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Residues in contact with SER 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASN* 3.0 29.3 + - - +
6B PRO* 3.8 14.7 - - - +
7B THR* 1.3 82.3 + - - +
9B ALA* 1.3 58.8 + - - -
11B VAL* 3.4 8.7 + - - +
12B LYS* 3.6 3.6 + - - +
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Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 4.5 15.0 - - + -
6B PRO* 2.9 22.4 + - + +
8B SER* 1.3 76.4 - - - +
10B LEU* 1.3 66.8 + - - +
12B LYS* 3.3 10.3 + - - +
13B GLU* 3.0 21.5 + - - +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 5.0 16.4 - - + +
6B PRO 3.0 11.8 + - - +
7B THR* 2.9 17.1 + - + +
9B ALA* 1.3 75.8 - - - +
11B VAL* 1.4 54.4 + - - +
13B GLU* 3.2 8.5 + - - +
14B THR* 2.7 50.3 + - - +
67B ARG* 6.2 1.1 - - - +
70B LYS* 5.9 0.7 - - - +
71B ASN* 3.3 36.8 - - - +
74B LEU* 4.5 21.5 - - + -
75B ILE* 3.9 22.7 - - + -
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.2 39.7 - - + +
107A MET* 4.5 26.7 - - + -
108A ASN* 3.5 23.1 - - + +
7B THR* 2.8 24.4 + - - +
8B SER* 3.6 9.2 - - - +
9B ALA 3.3 0.4 - - - -
10B LEU* 1.4 68.4 - - - +
12B LYS* 1.3 52.3 + - - +
14B THR* 2.9 12.7 + - - -
15B LEU* 2.8 36.1 + - + +
75B ILE* 4.5 13.7 - - + -
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASN* 3.3 28.0 - - - +
109A THR* 5.8 2.9 - - - -
8B SER 3.6 8.2 + - - +
9B ALA* 3.3 13.5 - - - +
11B VAL* 1.3 79.6 - - - +
13B GLU* 1.3 60.2 + - - +
15B LEU* 3.8 24.0 - - + +
16B ALA* 3.8 7.1 + - - +
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 5.1 9.7 - - - +
9B ALA 3.0 12.6 + - - +
10B LEU* 3.5 10.9 - - - +
12B LYS* 1.3 73.5 - - - +
14B THR* 1.4 56.3 + - - +
15B LEU 3.1 1.3 - - - -
16B ALA* 2.7 37.1 + - + +
17B LEU* 3.1 23.1 + - + +
67B ARG* 3.1 41.4 + - - +
71B ASN* 3.0 24.2 + - - -
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Residues in contact with THR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.1 13.0 - - + -
10B LEU* 2.7 32.3 + - - +
11B VAL* 2.9 8.0 + - - -
13B GLU* 1.4 69.6 - - - +
15B LEU* 1.3 62.5 + - - +
17B LEU* 3.5 11.6 + - - +
18B LEU* 3.3 21.4 + - + +
68B LEU* 4.2 12.1 - - + -
71B ASN* 2.9 26.2 + - + +
72B LEU* 4.1 26.7 - - + -
75B ILE* 3.9 8.8 - - + +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLN* 4.0 37.7 - - + +
104A LEU* 4.0 25.1 - - + +
105A GLY* 4.4 7.2 - - - +
108A ASN* 5.3 4.0 - - + +
109A THR* 5.8 0.9 - - - +
11B VAL* 2.8 25.5 + - + +
12B LYS* 3.8 23.3 - - + +
14B THR* 1.3 77.5 - - - +
16B ALA* 1.3 58.7 + - - +
17B LEU 3.3 0.3 + - - -
18B LEU* 3.3 11.1 + - + +
19B SER* 2.8 20.8 + - - +
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Residues in contact with ALA 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 LYS 3.8 6.5 + - - +
13B GLU* 2.7 24.6 + - + +
15B LEU* 1.3 73.2 - - - +
17B LEU* 1.3 54.6 + - + +
19B SER* 3.2 9.9 - - - -
20B THR* 3.1 32.5 + - + +
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Residues in contact with LEU 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 GLU* 3.1 40.2 + - + +
14B THR* 3.8 13.7 - - - +
15B LEU 3.4 0.2 - - - -
16B ALA* 1.3 72.3 - - + +
18B LEU* 1.3 67.2 + - - +
19B SER 3.1 1.6 - - - -
20B THR* 3.5 6.5 + - - +
21B HIS* 2.8 49.2 + - + +
64B THR* 4.6 4.7 - - - +
67B ARG* 4.0 29.2 - - + +
68B LEU* 3.9 23.9 - - + +
71B ASN* 4.1 1.8 - - - +
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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
----------------------------------------------------------
97A LEU* 3.8 40.4 - - + +
100A LEU* 4.2 16.8 - - + -
101A GLN* 3.9 29.8 - - + +
104A LEU* 4.7 15.5 - - + -
14B THR* 3.3 10.1 + - + +
15B LEU* 3.4 12.1 - - + +
17B LEU* 1.3 77.0 - - - +
19B SER* 1.3 63.7 - - - +
21B HIS* 3.2 14.0 + - - +
22B ARG* 3.3 23.4 + - + +
25B LEU* 4.5 2.7 - - + +
68B LEU* 3.9 27.3 - - + +
72B LEU* 5.4 3.8 - - + -
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLN* 5.7 5.7 + - - +
15B LEU 2.8 16.2 + - - -
16B ALA* 3.2 16.2 - - - -
18B LEU* 1.3 80.4 - - - +
20B THR* 1.3 59.4 + - - -
21B HIS 3.2 1.7 + - - -
22B ARG* 3.8 19.9 + - - +
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Residues in contact with THR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 3.1 19.0 + - + +
17B LEU* 3.5 13.0 + - - +
19B SER* 1.3 72.3 - - - +
21B HIS* 1.4 73.4 + - - +
22B ARG 3.8 0.4 - - - -
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Residues in contact with HIS 21 (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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17B LEU* 2.8 44.1 + - + +
18B LEU 3.2 6.7 + - - +
20B THR* 1.4 92.2 + - - +
22B ARG* 1.3 61.0 + - - +
23B THR 3.4 3.0 + - - -
24B LEU* 3.4 14.6 + - + +
25B LEU* 3.0 37.3 + - + +
64B THR* 3.3 36.1 + - - -
65B VAL* 4.0 31.2 - - + -
68B LEU* 4.5 4.2 - - + +
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Residues in contact with ARG 22 (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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94A ASN* 3.5 39.0 + - - +
97A LEU* 3.7 24.7 - - + +
98A ASP* 3.8 11.6 + - - -
101A GLN* 3.4 25.4 + - - -
18B LEU* 3.3 23.5 + - + +
19B SER* 3.8 14.7 + - - +
20B THR 3.8 1.2 - - - -
21B HIS* 1.3 77.4 - - - +
23B THR* 1.3 50.7 + - - +
25B LEU* 4.2 6.3 - - - -
26B ILE* 2.7 52.5 + - + +
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Residues in contact with THR 23 (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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21B HIS 3.4 0.6 - - - -
22B ARG* 1.3 73.1 + - - +
24B LEU* 1.3 70.1 + - - +
26B ILE* 3.7 15.1 - - + +
27B ALA* 3.1 22.9 + - - +
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Residues in contact with LEU 24 (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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21B HIS* 3.4 18.1 + - + +
23B THR* 1.3 83.2 - - - +
25B LEU* 1.4 65.6 + - + +
27B ALA* 3.2 17.2 - - + +
28B ASN 4.6 0.3 + - - -
59B THR* 4.2 14.6 - - + -
60B VAL* 4.8 20.2 - - + +
65B VAL* 3.7 42.4 - - + -
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Residues in contact with LEU 25 (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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93A VAL* 3.4 15.5 - - + +
97A LEU* 4.0 33.0 - - + -
18B LEU* 4.5 5.8 - - + +
21B HIS* 3.0 30.6 + - + +
22B ARG* 3.7 7.4 - - - +
24B LEU* 1.4 77.9 - - + +
26B ILE* 1.3 60.4 + - - +
27B ALA 3.4 0.3 + - - -
28B ASN* 3.9 10.9 + - - +
55B LEU* 3.9 30.3 - - + +
59B THR* 4.2 19.7 - - + +
65B VAL* 4.7 6.3 - - + -
68B LEU* 4.0 22.4 - - + -
69B PHE* 4.3 12.3 - - + -
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Residues in contact with ILE 26 (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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93A VAL* 4.2 11.0 - - + +
94A ASN* 3.9 35.9 - - + +
97A LEU* 4.7 3.4 - - + -
22B ARG* 2.7 48.8 + - + +
23B THR* 3.7 20.6 - - + +
25B LEU* 1.3 72.1 - - + +
27B ALA* 1.3 64.4 + - - +
28B ASN 2.9 16.4 + - - +
29B GLU* 3.8 15.0 - - - +
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Residues in contact with ALA 27 (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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23B THR 3.1 13.6 + - - +
24B LEU* 3.2 20.1 + - + +
26B ILE* 1.3 77.6 - - - +
28B ASN* 1.3 56.8 + - - +
29B GLU* 3.2 13.8 + - - +
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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
------------------------------------------------------------
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