Contacts of the strand formed by residues 5 - 15 (chain G) in PDB entry 1U3H
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 HIS 5 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3G ALA* 3.2 2.3 - - - +
4G ASP* 1.3 103.2 + - + +
6G VAL* 1.3 69.2 + - - +
26G PHE* 4.1 15.7 - + + -
27G ASP* 2.8 30.1 + - - +
17H PHE* 2.8 45.7 + - + -
20H GLY 6.0 1.6 - - - -
83H TYR* 3.8 21.7 + + + -
91H LEU* 3.5 22.7 - - + +
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Residues in contact with VAL 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G ALA* 4.3 10.8 - - + +
5G HIS* 1.3 82.2 - - - +
7G GLY* 1.3 63.9 + - - +
8G SER* 4.1 1.7 + - - +
25G GLU 4.1 0.9 - - - +
26G PHE* 3.5 6.2 - - - -
27G ASP* 2.9 42.5 + - - +
28G GLY 4.8 0.2 + - - -
14H PHE* 4.0 21.1 - - + -
15H CYS 3.3 5.2 - - - +
16H TYR* 3.6 37.9 - - + -
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Residues in contact with GLY 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G VAL* 1.3 74.7 - - - +
8G SER* 1.3 60.9 + - - -
9G TYR* 3.7 23.8 + - - -
25G GLU 3.6 5.6 - - - -
26G PHE* 4.2 5.6 - - - -
14H PHE* 3.3 3.0 - - - -
15H CYS* 2.6 49.6 + - - +
17H PHE* 4.1 2.7 - - - -
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Residues in contact with SER 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G VAL* 4.1 2.5 + - - +
7G GLY* 1.3 68.7 - - - -
9G TYR* 1.3 66.9 + - - +
10G ILE* 3.8 25.9 - - - +
23G THR 3.9 1.6 - - - +
24G PHE* 3.3 2.1 - - - +
25G GLU* 2.8 43.5 + - - -
139G VAL* 5.3 0.5 - - - +
13H PRO* 2.8 22.6 + - - -
14H PHE* 3.5 24.4 - - - -
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Residues in contact with TYR 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLY* 3.7 16.5 + - - -
8G SER* 1.3 72.1 - - - +
9G GLY* 1.3 57.7 + - - +
24G PHE* 3.4 31.4 - + + -
25G GLU 4.6 0.7 - - - -
26G PHE* 3.7 9.1 - + - -
31G LEU* 4.4 7.4 - - + -
52G ARG* 4.3 5.6 - - - -
13H PRO* 3.7 12.2 - - - +
15H CYS* 3.6 33.6 - - + -
17H PHE* 4.2 6.6 - + - -
78H VAL* 3.9 12.1 - - + -
79H CYS* 4.5 2.2 - - - -
82H ASN* 3.0 44.8 - - + +
86H GLU* 2.9 42.2 + - - +
0I GLY 3.8 2.7 - - - +
1I ALA* 3.6 1.2 - - - -
2I SER* 3.0 23.7 + - - +
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Residues in contact with GLY 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G SER 3.2 2.4 + - - -
9G TYR* 1.3 76.4 - - - +
10G ILE* 1.3 67.4 + - - +
11G VAL* 3.3 8.7 + - - +
22G TYR* 3.6 25.0 - - - -
23G THR 3.5 4.3 - - - -
24G PHE* 3.2 12.9 - - - -
11H PHE* 3.5 19.9 - - - -
13H PRO* 3.8 5.1 - - - +
1I ALA* 4.8 0.2 - - - -
2I SER 4.6 2.6 - - - +
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Residues in contact with ILE 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G SER* 3.8 25.8 - - - +
9G GLY* 1.3 72.9 - - - +
11G VAL* 1.3 67.3 + - - +
12G VAL* 4.3 11.7 - - + -
21G GLN* 3.6 3.4 + - - +
22G TYR* 3.3 8.0 - - - -
23G THR* 2.8 46.6 + - - +
25G GLU* 3.3 35.9 - - + +
137G PHE 6.1 0.4 - - - +
139G VAL* 3.9 32.1 - - + -
10H GLN* 6.3 0.2 - - + -
11H PHE 3.3 13.0 - - - +
12H GLN* 4.5 5.8 - - + -
13H PRO* 3.9 8.1 - - + -
14H PHE* 6.1 0.2 - - + -
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Residues in contact with VAL 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G GLY 3.3 13.7 + - - +
10G ILE* 1.3 71.6 - - - +
12G VAL* 1.3 77.7 + - - +
13G TYR* 4.6 1.1 - - + +
21G GLN 3.7 2.0 - - - -
22G TYR* 3.7 23.3 - - + -
62G ASN* 3.8 31.6 - - + +
63G ILE* 4.1 13.2 - - + -
66G GLY* 4.4 7.4 - - - -
9H VAL* 5.8 0.4 - - + +
10H GLN* 3.4 4.0 - - - +
11H PHE* 2.9 45.9 + - + +
4I TYR* 3.9 19.5 - - + -
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Residues in contact with VAL 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ILE* 4.3 13.9 - - + -
11G VAL* 1.3 83.2 - - - +
13G TYR* 1.3 62.0 + - - +
14G GLN* 4.5 10.1 - - - +
19G ILE 3.7 0.3 - - - +
20G GLY* 3.1 6.1 - - - -
21G GLN* 3.0 52.5 + - + +
63G ILE* 4.6 0.7 - - - +
115G PRO* 4.3 19.5 - - + -
137G PHE* 6.1 0.9 - - + -
145G PHE* 3.9 25.8 - - + -
8H VAL* 4.1 18.2 - - + -
9H VAL 3.6 4.9 - - - +
10H GLN* 4.6 5.2 - - + +
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Residues in contact with TYR 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G VAL* 4.3 2.0 - - + -
12G VAL* 1.3 73.9 - - - +
14G GLN* 1.3 67.1 + - - +
15G SER* 5.5 0.9 - - - -
18G ASP* 2.8 59.1 + - + +
19G ILE 3.6 1.3 - - - -
20G GLY* 4.4 9.4 - - - -
63G ILE* 3.5 40.8 - - + -
66G GLY* 3.8 17.9 - - - -
67G LYS* 3.3 43.3 + - + +
70G LEU* 3.6 16.3 - - + +
8H VAL* 3.0 2.9 - - - +
9H VAL* 2.8 43.6 + - + +
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Residues in contact with GLN 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G VAL* 4.5 6.6 - - - +
13G TYR* 1.3 73.3 - - - +
15G SER* 1.3 57.8 + - - +
16G PRO 4.5 0.2 - - - -
18G ASP* 3.4 6.4 + - - -
19G ILE* 3.0 68.2 + - + +
20G GLY* 5.8 0.6 - - - -
70G LEU* 3.7 5.4 - - - -
115G PRO* 3.5 43.3 + - - +
116G VAL* 3.9 7.9 - - - +
137G PHE* 6.0 0.2 - - - -
6H HIS* 3.1 26.3 + - + +
7H PHE 3.1 17.0 - - - +
8H VAL* 3.3 20.4 - - + +
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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