Contacts of the strand formed by residues 7 - 18 (chain H) 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 PHE 7 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G GLN* 3.1 7.1 - - - +
15G SER* 2.9 46.0 + - - +
16G PRO* 5.5 0.9 - - + -
70G LEU* 4.0 16.2 - - + -
74G THR* 3.9 18.2 - - + +
79G SER* 3.5 25.8 - - - -
80G THR 3.4 21.1 - - - -
81G PRO* 3.4 21.5 - - + -
1H GLY* 3.8 18.8 - - - -
5H ARG* 3.6 33.2 - - + -
6H HIS* 1.3 79.7 - - - +
8H VAL* 1.3 62.5 + - - +
32H TYR* 3.4 9.9 - - - +
33H ASN* 3.8 3.8 - - - -
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Residues in contact with VAL 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G VAL* 4.1 12.8 - - + -
13G TYR 3.0 24.5 - - - +
14G GLN* 3.3 24.2 - - + +
70G LEU* 3.5 4.4 - - - +
82G ALA* 5.0 3.4 - - + -
113G PHE* 4.6 13.0 - - + -
114G PRO* 5.1 5.2 - - + -
115G PRO* 5.2 4.0 - - + -
6H HIS* 4.9 0.9 - - + -
7H PHE* 1.3 78.4 - - - +
9H VAL* 1.3 74.2 - - - +
10H GLN* 5.0 3.8 - - + +
32H TYR* 2.1 29.1 - - - +
33H ASN* 3.2 32.7 + - - +
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Residues in contact with VAL 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G VAL* 5.8 0.2 - - + -
12G VAL* 3.6 1.4 - - - -
13G TYR* 2.8 44.2 + - + +
66G GLY* 3.5 25.1 - - - +
69G ASN* 4.2 5.2 - - + +
70G LEU* 3.4 33.0 - - + +
73G LEU* 4.5 4.9 - - + -
8H VAL* 1.3 80.8 - - - +
10H GLN* 1.3 69.8 + - - +
31H ILE 3.5 4.7 - - - +
32H TYR* 3.0 19.5 - - + +
37H TYR* 5.7 0.7 - - - +
4I TYR* 3.7 18.8 - - + +
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Residues in contact with GLN 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ILE* 6.1 0.2 - - - +
11G VAL 3.4 5.4 - - - +
12G VAL* 4.6 7.5 - - + +
113G PHE* 4.2 1.6 - - - -
139G VAL* 4.7 0.3 - - - +
143G TYR* 3.1 25.1 + - - +
145G PHE* 3.4 32.7 - - + -
8H VAL* 5.0 4.2 - - + +
9H VAL* 1.3 81.4 - - - +
11H PHE* 1.3 61.1 + - - +
12H GLN* 2.9 33.3 + - + +
29H ARG 3.5 3.3 - - - +
30H TYR* 3.8 1.4 - - - -
31H ILE* 2.9 60.3 + - + +
33H ASN 3.2 22.7 + - - +
4I TYR* 4.2 5.3 + - - -
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Residues in contact with PHE 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G GLY 3.5 17.9 - - - -
10G ILE* 3.3 9.2 - - - +
11G VAL* 2.9 37.3 + - + +
10H GLN* 1.3 73.4 - - - +
12H GLN* 1.3 60.9 + - - +
13H PRO* 3.9 20.4 - - + -
28H THR* 3.6 26.9 - - + -
29H ARG 3.6 6.7 - - - -
30H TYR* 3.5 27.6 - + - -
2I SER* 3.7 24.5 - - - -
3I GLN 3.5 15.7 - - - -
4I TYR* 3.2 53.3 + + + -
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Residues in contact with GLN 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ILE* 4.5 6.5 - - + -
139G VAL* 3.5 35.6 - - + +
140G ASN 4.6 2.3 - - - +
143G TYR* 3.6 31.5 - - - +
10H GLN* 2.9 30.4 + - + +
11H PHE* 1.3 79.9 - - - +
13H PRO* 1.3 62.5 - - - +
14H PHE* 3.2 41.4 - - + -
27H VAL 3.9 0.2 - - - +
29H ARG* 3.1 34.6 + - + +
31H ILE* 4.5 6.2 - - + +
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Residues in contact with PRO 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLY 4.3 0.4 - - - -
8G SER* 2.8 26.2 + - - -
9G TYR 3.7 48.2 - - - +
10G ILE* 3.9 5.4 - - + +
11H PHE* 3.7 19.5 - - + +
12H GLN* 1.3 86.3 - - - +
14H PHE* 1.3 59.8 + - - +
15H CYS* 6.4 0.4 - - - -
26H TYR* 4.7 1.1 - - + -
27H VAL 3.6 6.7 - - - +
28H THR* 4.5 4.7 - - - +
2I SER* 3.4 28.9 - - - +
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Residues in contact with PHE 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G VAL* 4.0 15.9 - - + -
7G GLY 3.3 3.1 - - - -
8G SER* 3.5 19.3 - - - -
10G ILE* 6.1 0.2 - - + -
139G VAL* 4.6 11.4 - - + -
143G TYR* 5.8 0.4 - + - -
12H GLN* 3.2 59.7 - - + -
13H PRO* 1.3 71.6 - - - +
15H CYS* 1.3 62.2 + - - +
16H TYR* 3.4 35.0 - - + -
26H TYR* 3.2 9.8 - - - -
27H VAL* 2.8 39.3 + - + +
29H ARG* 3.7 28.0 - - + -
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Residues in contact with CYS 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G VAL* 3.3 5.5 - - - -
7G GLY 2.6 39.1 + - - +
9G TYR* 3.6 21.5 - - - -
13H PRO* 6.4 0.2 - - - -
14H PHE* 1.3 73.9 - - - +
16H TYR* 1.3 61.5 + - - +
17H PHE* 3.4 25.0 - - + -
24H ILE* 5.7 0.7 - - + -
25H ARG 3.8 1.8 - - - -
26H TYR* 4.2 4.9 - - - -
78H VAL* 4.7 2.0 - - - -
79H CYS* 2.0 55.2 - - - -
2I SER* 5.1 1.6 - - - -
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Residues in contact with TYR 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ILE* 4.0 47.4 + - + +
3G ALA* 3.8 12.3 - - + -
5G HIS 3.7 2.5 - - - -
6G VAL* 3.6 32.8 - - + -
14H PHE* 3.4 39.8 - - + -
15H CYS* 1.3 68.8 - - - +
17H PHE* 1.3 62.4 + - - +
18H THR* 4.9 1.2 + - - -
23H ARG* 3.9 1.2 - - - +
24H ILE* 3.4 7.4 - - - +
25H ARG* 2.8 52.4 + - + +
27H VAL* 3.9 22.7 - - + -
29H ARG* 4.0 13.7 + - - -
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Residues in contact with PHE 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ALA* 3.0 2.9 - - - +
4G ASP* 2.8 26.6 + - - +
5G HIS* 2.8 31.1 + - + +
7G GLY 4.1 7.0 - - - -
9G TYR* 4.2 12.3 - - - -
26G PHE* 4.5 3.1 - + - -
15H CYS* 3.4 41.7 - - + -
16H TYR* 1.3 74.1 - - - +
18H THR* 1.3 61.7 + - - +
19H ASN 4.4 0.2 - - - -
20H GLY 3.7 12.8 - - - +
21H THR* 4.7 0.7 - - + -
23H ARG 3.9 1.6 - - - -
24H ILE* 4.0 26.9 - - + -
79H CYS* 3.3 35.7 - - + -
80H ARG* 4.3 0.4 - - - -
83H TYR* 3.4 42.2 - + + -
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Residues in contact with THR 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G GLU* 4.2 2.9 + - - +
3G ALA* 3.8 15.3 - - - +
4G ASP* 3.8 13.2 - - - +
16H TYR 4.9 1.2 + - - -
17H PHE* 1.3 78.0 + - - +
19H ASN* 1.3 81.6 + - + +
20H GLY 3.5 2.9 + - - +
23H ARG* 3.1 66.5 + - + +
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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
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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