Contacts of the helix formed by residues 2 - 20 (chain B) in PDB entry 5UUP
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 GLY 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A CYS* 4.0 0.2 - - - +
59A VAL* 5.8 1.3 - - - -
1B AKR 1.3 79.1 - - - +
3B VAL* 1.3 67.7 + - - -
4B ARG* 3.2 20.6 + - - -
5B GLU* 2.9 7.9 + - - -
6B ILE* 3.0 30.3 + - - +
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Residues in contact with VAL 3 (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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70A LEU* 3.9 24.9 - - + -
73A GLN* 3.9 46.0 - - + +
74A VAL* 4.1 9.3 - - + +
77A LYS* 4.2 13.7 - - + -
2B GLY* 1.3 71.0 - - - -
4B ARG* 1.3 74.9 + - + +
6B ILE* 3.3 7.5 + - - +
7B ALA* 2.8 29.1 + - - +
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Residues in contact with ARG 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 5.5 9.0 - - + -
2B GLY* 3.2 25.7 - - - -
3B VAL* 1.3 94.2 - - + +
5B GLU* 1.3 73.6 + - - +
7B ALA* 3.2 1.7 + - - -
8B TYR* 2.9 52.6 + - + -
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Residues in contact with GLU 5 (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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52A LEU* 4.0 10.3 - - + +
55A CYS* 3.9 5.8 - - - -
1B AKR 3.8 28.3 - - + +
2B GLY* 2.9 23.3 + - - +
4B ARG* 1.3 89.0 + - + +
6B ILE* 1.3 57.4 + - - +
8B TYR* 5.2 1.6 - - - -
9B GLY* 2.9 27.8 + - - +
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Residues in contact with ILE 6 (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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48A VAL* 6.0 0.9 - - + -
52A LEU* 3.8 14.9 - - + +
55A CYS* 4.2 17.5 - - + -
56A LEU* 4.0 24.0 - - + -
59A VAL* 4.1 20.6 - - + -
70A LEU* 5.3 6.7 - - + -
74A VAL* 4.0 15.0 - - + -
95A PHE* 3.8 28.3 - - + -
2B GLY* 3.0 24.6 + - - +
3B VAL* 3.6 6.3 - - - +
5B GLU* 1.3 76.4 - - - +
7B ALA* 1.3 58.4 + - - +
9B GLY 3.3 0.9 + - - -
10B LEU* 2.8 39.8 + - + +
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Residues in contact with ALA 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.4 37.2 - - + +
77A LYS* 3.5 23.3 - - + -
78A GLU* 3.9 9.0 - - - +
3B VAL 2.8 21.6 + - - +
4B ARG 3.9 2.2 - - - +
6B ILE* 1.3 72.9 - - - +
8B TYR* 1.3 60.1 + - + +
10B LEU* 3.2 6.0 + - - +
11B ARG* 2.9 25.8 + - - +
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Residues in contact with TYR 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 3.8 25.1 - - + +
80A GLU* 2.7 33.3 + - - -
4B ARG* 2.9 49.0 + - + +
5B GLU* 4.7 1.8 - - - +
7B ALA* 1.3 73.5 - - - +
9B GLY* 1.3 59.9 + - - +
11B ARG* 3.7 38.9 - - - +
12B ARG* 3.0 31.4 + - - +
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Residues in contact with GLY 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 5.2 2.0 - - - +
52A LEU* 4.4 15.7 - - - -
5B GLU 2.9 21.7 + - - -
6B ILE 3.6 0.7 - - - -
8B TYR* 1.3 75.0 - - - +
10B LEU* 1.3 63.0 + - - +
12B ARG* 3.4 6.6 + - - +
13B ALA* 3.1 23.4 + - - +
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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
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48A VAL* 3.9 33.2 - - + -
74A VAL* 3.6 31.4 - - + -
75A MET* 4.1 1.6 - - + -
78A GLU* 3.7 20.4 - - - +
91A THR* 3.7 23.0 - - + +
94A ALA* 5.5 1.8 - - + -
95A PHE* 3.9 31.2 - - + +
98A ILE* 5.3 0.9 - - + -
6B ILE* 2.8 22.0 + - + +
7B ALA 3.4 7.0 - - - +
9B GLY* 1.3 71.2 - - - +
11B ARG* 1.3 66.8 + - - +
13B ALA* 3.2 4.6 + - - +
14B ALA* 2.9 23.9 + - - +
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Residues in contact with ARG 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS 2.8 26.6 + - - -
78A GLU* 2.9 31.1 + - + +
80A GLU* 3.4 19.4 + - - +
81A ASP* 3.4 25.8 + - - +
88A ARG* 3.3 30.3 - - - +
7B ALA 2.9 16.4 + - - +
8B TYR* 3.7 29.4 - - - +
9B GLY 3.3 0.2 - - - -
10B LEU* 1.3 75.9 - - - +
12B ARG* 1.3 61.3 + - - +
14B ALA* 3.1 4.1 + - - +
15B ASP* 3.0 30.1 + - - +
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Residues in contact with ARG 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 TYR 3.0 19.0 + - - +
9B GLY* 3.8 6.7 - - - +
10B LEU 3.2 0.2 - - - -
11B ARG* 1.3 77.0 - - + +
13B ALA* 1.3 61.7 + - - +
15B ASP* 3.6 4.7 + - - +
16B ASP* 3.2 46.6 + - - +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.6 9.2 - - + -
47A GLU* 5.8 7.2 - - + -
48A VAL* 4.1 23.3 - - + -
51A ASN* 6.2 1.8 - - - +
91A THR* 4.5 2.0 - - + -
9B GLY 3.1 16.9 + - - +
10B LEU 3.7 3.6 - - - +
12B ARG* 1.3 76.1 - - - +
14B ALA* 1.3 62.2 + - - +
16B ASP* 3.6 6.6 + - - +
17B VAL* 3.0 29.7 + - + +
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Residues in contact with ALA 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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78A GLU* 4.1 1.6 - - - +
87A GLY* 3.4 27.9 - - - +
88A ARG* 3.4 26.2 - - + +
91A THR* 3.5 9.6 - - + +
10B LEU 2.9 13.2 + - - +
11B ARG 3.4 8.1 - - - +
13B ALA* 1.3 72.7 - - - +
15B ASP* 1.3 58.4 + - - +
16B ASP 3.0 1.6 - - - -
17B VAL* 2.9 6.2 + - - +
18B ASN* 2.7 34.1 + - - +
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Residues in contact with ASP 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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83A ILE* 6.0 0.2 - - - -
85A ASN* 3.3 16.3 + - - +
88A ARG* 3.2 39.5 + - - +
11B ARG* 3.0 24.6 + - - +
12B ARG* 4.3 4.3 - - - +
14B ALA* 1.3 74.9 - - - +
16B ASP* 1.3 59.9 + - - +
18B ASN* 3.8 6.9 + - - +
19B ALA* 3.0 29.3 + - - +
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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 ARG* 3.2 35.2 + - - +
13B ALA* 3.7 6.4 - - - +
14B ALA 3.0 0.8 - - - -
15B ASP* 1.3 76.6 - - - +
17B VAL* 1.3 67.0 + - + +
19B ALA* 3.2 5.9 + - - +
20B GLN* 3.0 42.6 + - - +
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Residues in contact with VAL 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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40A VAL* 4.5 11.4 - - + -
44A VAL* 3.6 28.0 - - + -
87A GLY* 4.1 12.3 - - - +
90A VAL* 5.1 2.2 - - + -
148A PHE* 3.9 24.7 - - + -
13B ALA* 3.0 18.6 + - + +
14B ALA* 2.9 10.4 + - - +
16B ASP* 1.3 73.8 - - - +
18B ASN* 1.3 66.2 + - - +
20B GLN* 3.1 18.7 + - - +
21B VAL* 3.6 12.5 + - + +
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Residues in contact with ASN 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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85A ASN* 3.5 34.9 - - - +
86A TRP* 3.4 16.1 + - - +
87A GLY* 3.3 18.4 + - - +
148A PHE* 5.2 0.4 - - - -
14B ALA 2.7 18.3 + - - +
15B ASP* 3.8 6.7 - - - +
17B VAL* 1.3 72.9 - - - +
19B ALA* 1.3 63.4 + - - +
20B GLN 3.1 1.6 + - - -
21B VAL* 3.1 18.2 + - - +
22B GLU* 2.9 42.2 + - - +
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Residues in contact with ALA 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 ASP 3.0 20.0 + - - +
16B ASP* 3.7 6.3 - - - +
18B ASN* 1.3 76.2 - - - +
20B GLN* 1.3 58.6 + - + +
21B VAL 3.2 3.7 + - - -
22B GLU* 3.3 16.6 + - - +
23B ARG* 2.9 26.9 + - - +
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Residues in contact with GLN 20 (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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16B ASP* 3.0 34.4 + - - +
17B VAL* 3.7 8.0 - - - +
18B ASN 3.1 1.0 + - - -
19B ALA* 1.3 78.8 - - + +
21B VAL* 1.3 66.3 + - + +
22B GLU 3.7 0.2 - - - -
23B ARG* 4.7 13.5 + - - +
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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