Contacts of the strand formed by residues 7 - 18 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLN* 3.1 3.0 - - - +
15C SER* 2.7 55.9 + - - +
16C PRO* 5.4 0.7 - - + -
70C LEU* 3.9 15.1 - - + +
74C THR* 3.7 17.9 - - + +
79C SER* 3.4 36.3 - - - -
80C THR 3.4 6.7 - - - -
81C PRO* 3.4 21.3 - - + -
1D GLY* 4.1 14.6 - - - -
5D ARG* 3.0 45.8 - - + -
6D HIS* 1.3 75.5 - - - +
8D VAL* 1.3 59.0 + - - +
32D TYR* 3.2 20.2 - - - +
33D ASN* 3.8 3.6 - - - -
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Residues in contact with VAL 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 3.9 16.2 - - + -
13C TYR 3.2 17.7 - - - +
14C GLN* 3.4 21.5 - - + +
70C LEU* 3.7 2.7 - - - +
82C ALA* 4.9 0.9 - - + -
113C PHE* 4.5 13.5 - - + -
114C PRO* 4.8 0.2 - - + -
115C PRO* 4.7 8.7 - - + -
6D HIS* 4.4 9.6 - - + +
7D PHE* 1.3 75.5 - - - +
9D VAL* 1.3 80.2 - - - +
10D GLN* 4.8 4.5 - - + +
32D TYR* 2.2 28.6 - - - +
33D ASN* 3.3 30.9 + - - +
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Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 5.6 0.7 - - + +
12C VAL* 3.5 3.3 - - - -
13C TYR* 2.9 38.5 + - + +
66C GLY* 3.6 24.2 - - - +
69C ASN* 4.5 3.8 - - + +
70C LEU* 3.3 37.5 - - + +
73C LEU* 4.7 3.4 - - + -
8D VAL* 1.3 78.3 - - - +
10D GLN* 1.3 63.4 + - - +
31D ILE 3.6 5.6 - - - +
32D TYR* 3.0 20.9 - - + +
37D TYR* 5.9 0.7 - - - +
4P TYR* 3.6 20.2 - - + +
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Residues in contact with GLN 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 6.3 0.2 - - + -
11C VAL 3.3 5.2 - - - +
12C VAL* 4.6 4.6 - - + +
113C PHE* 4.0 1.8 - - - -
139C VAL* 4.8 0.2 - - - +
143C TYR* 3.0 27.4 + - - +
145C PHE* 3.2 33.6 - - + -
8D VAL* 4.8 5.5 - - + +
9D VAL* 1.3 79.5 - - - +
11D PHE* 1.3 60.1 + - - +
12D GLN* 3.0 32.5 + - + +
29D ARG 3.7 1.4 - - - +
30D TYR* 3.8 1.7 - - - -
31D ILE* 2.8 58.7 + - + +
33D ASN 3.2 23.0 + - - +
4P TYR* 4.2 5.8 + - - -
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Residues in contact with PHE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLY 3.2 22.9 - - - -
10C ILE* 3.3 12.0 - - - +
11C VAL* 2.8 35.5 + - + -
10D GLN* 1.3 73.6 - - - +
12D GLN* 1.3 63.7 + - - +
13D PRO* 3.8 11.2 - - + -
28D THR* 3.0 34.3 - - + -
29D ARG 3.6 7.6 - - - -
30D TYR* 3.7 12.1 - + - -
2P SER* 3.4 33.4 - - - -
3P GLN 3.4 17.5 - - - -
4P TYR* 3.2 50.5 + + + -
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Residues in contact with GLN 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.3 4.9 - - + -
139C VAL* 3.5 36.0 - - + +
140C ASN 4.5 2.6 + - - +
143C TYR* 3.7 31.8 - - - +
10D GLN* 3.0 31.0 + - + +
11D PHE* 1.3 83.0 - - - +
13D PRO* 1.3 63.2 - - - +
14D PHE* 3.3 40.7 - - + -
27D VAL 3.7 0.2 - - - +
29D ARG* 3.0 39.1 + - + -
31D ILE* 4.8 2.6 - - + +
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Residues in contact with PRO 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLY 4.3 0.2 - - - -
8C SER* 2.9 26.6 + - - -
9C TYR 3.7 50.0 - - - +
10C ILE* 3.9 5.6 - - + +
11D PHE* 3.7 16.2 - - + +
12D GLN* 1.3 87.3 - - - +
14D PHE* 1.3 62.5 + - - +
15D CYS* 6.1 0.2 - - - -
26D TYR* 4.6 2.2 - - + +
27D VAL 3.5 4.9 - - - +
28D THR* 4.4 3.8 - - - +
2P SER* 3.2 33.0 - - - +
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Residues in contact with PHE 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C VAL* 3.9 20.2 - - + -
7C GLY 3.5 1.3 - - - -
8C SER* 3.4 20.2 - - - -
10C ILE* 6.1 0.2 - - + -
139C VAL* 4.6 12.1 - - + -
12D GLN* 3.3 57.2 - - + -
13D PRO* 1.3 72.8 - - - +
15D CYS* 1.3 62.8 + - - +
16D TYR* 3.6 33.0 - + + -
25D ARG 3.5 1.6 - - - +
26D TYR* 3.3 10.4 - - - -
27D VAL* 2.6 42.2 + - + +
29D ARG* 3.6 26.0 - - - -
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Residues in contact with CYS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C VAL* 3.5 1.9 - - - -
7C GLY 2.7 35.0 + - - +
9C TYR* 3.8 21.8 - - + -
13D PRO 6.1 0.2 - - - -
14D PHE* 1.3 73.6 - - - +
16D TYR* 1.3 59.3 + - - +
17D PHE* 3.0 29.2 - - + -
24D ILE* 5.1 0.9 - - + -
25D ARG 3.8 1.8 - - - -
26D TYR* 4.3 5.6 - - - -
78D VAL* 4.6 2.0 - - - -
79D CYS* 2.0 57.2 - - - -
2P SER* 5.1 1.6 - - - -
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Residues in contact with TYR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ILE* 3.7 43.2 + - + +
2C GLU 4.1 10.1 - - - +
3C ALA* 3.9 8.5 - - + -
5C HIS 3.8 3.1 - - - -
6C VAL* 3.8 33.7 - - + -
14D PHE* 3.6 32.3 - + + -
15D CYS* 1.3 69.4 - - - +
17D PHE* 1.3 61.1 + - - +
18D THR* 5.0 1.5 + - - +
23D ARG* 3.7 1.3 - - - +
24D ILE* 3.4 7.3 - - - +
25D ARG* 3.0 48.2 + - + +
27D VAL* 3.6 23.3 - - + -
29D ARG* 3.2 22.9 + - - -
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Residues in contact with PHE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ALA* 3.0 1.5 - - - +
4C ASP* 2.7 33.8 + - - +
5C HIS* 2.9 28.5 + - + +
6C VAL 4.9 0.2 - - - -
7C GLY* 4.2 8.5 - - - -
9C TYR* 4.7 7.4 - + - -
26C PHE* 4.8 2.0 - + - -
15D CYS* 3.0 48.2 - - + -
16D TYR* 1.3 73.4 - - - +
18D THR* 1.3 57.0 + - - +
19D ASN 4.2 0.2 - - - -
20D GLY 3.5 17.0 - - - +
21D THR* 4.1 2.2 - - + -
23D ARG 3.8 1.6 - - - -
24D ILE* 3.9 29.2 - - + -
79D CYS* 3.4 23.8 - - + -
83D TYR* 3.3 49.1 - + + -
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Residues in contact with THR 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GLU* 3.9 5.5 + - - +
3C ALA* 3.8 14.2 - - - +
4C ASP* 3.7 11.7 - - - +
16D TYR* 5.0 1.4 + - - +
17D PHE* 1.3 76.8 + - - +
19D ASN* 1.3 80.9 + - + +
20D GLY 3.6 1.1 + - - +
23D ARG* 2.9 69.1 + - + +
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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