Contacts of the strand formed by residues 3 - 12 (chain F) in PDB entry 5HHM
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 3 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F GLY* 2.8 38.0 + - - -
2F SER* 1.4 73.2 + - - +
4F SER* 1.3 62.0 + - - +
29F ASP* 3.1 30.1 - - - +
102F ASP* 3.3 4.9 - - - +
103F VAL* 2.9 46.6 + - + +
104F GLY 4.4 0.4 + - - -
107F TRP* 3.8 23.3 + + - -
168F LEU* 4.2 3.8 - - + -
172F LEU* 3.5 29.7 - - + +
179F LEU 4.3 9.7 + - - -
180F GLN* 5.0 11.0 + - + +
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Residues in contact with SER 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F HIS* 1.3 76.9 - - - +
5F MET* 1.3 60.3 + - - +
6F ARG* 3.9 19.9 + - - +
28F VAL* 3.4 4.9 - - - -
29F ASP* 2.8 54.0 + - - +
101F CYS 3.4 4.3 - - - -
102F ASP* 3.3 23.6 - - - -
168F LEU* 3.5 10.5 - - - +
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Residues in contact with MET 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F SER* 1.3 73.7 - - - +
6F ARG* 1.3 63.9 + - - +
7F TYR* 4.0 28.3 - - + -
27F TYR 3.3 9.9 - - - +
28F VAL* 4.6 1.3 - - + -
33F PHE* 4.4 3.8 - - + -
99F TYR 4.0 0.2 - - - +
100F GLY* 3.1 25.3 - - - -
101F CYS* 2.9 14.0 + - - +
159F TYR* 4.2 4.3 - - - +
164F CYS* 3.4 43.5 - - - +
167F TRP* 3.8 11.0 - - + -
168F LEU* 3.8 22.6 - - + +
171F TYR* 3.4 37.0 - - - -
1H GLY 4.2 1.6 - - - +
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Residues in contact with ARG 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F SER* 3.9 17.1 + - - +
5F MET* 1.3 75.8 + - - +
7F TYR* 1.3 66.2 + - - +
8F PHE* 3.6 27.0 - - + -
25F VAL 4.0 0.2 - - - +
26F GLY* 3.4 3.1 - - - -
27F TYR* 2.8 45.9 + - + +
29F ASP 5.9 1.1 - - - +
98F MET* 3.4 35.6 - - + +
99F TYR 3.7 2.9 - - - -
101F CYS 3.7 14.5 + - - +
102F ASP* 2.6 41.4 + - - -
113F TYR* 3.1 30.7 + - - -
58G LYS* 5.6 10.9 - - - +
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Residues in contact with TYR 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F MET* 4.0 18.8 - - + -
6F ARG* 1.3 75.5 - - - +
8F PHE* 1.3 61.4 + - - +
9F PHE* 3.6 24.0 - + + -
24F ALA* 6.4 1.1 - - + -
25F VAL 3.5 4.0 - - - -
26F GLY* 3.6 25.8 - - - -
33F PHE* 3.2 21.5 - + - -
34F VAL* 3.9 12.7 - - + +
45F MET* 5.0 1.8 - - + -
59F TYR* 4.8 0.9 + - - -
63F GLU* 4.4 1.9 + - - -
97F ARG 3.7 0.5 - - - +
98F MET* 3.1 9.7 - - - +
99F TYR* 3.0 49.7 + + + +
100F GLY* 5.9 0.7 - - - -
159F TYR* 4.0 3.8 - - - -
171F TYR* 4.0 0.2 + - - -
1H GLY* 2.8 43.5 + - - -
2H ILE* 3.4 26.7 + - + +
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Residues in contact with PHE 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ARG* 3.6 33.4 - - + -
7F TYR* 1.3 73.8 - - - +
9F PHE* 1.3 62.5 - - - +
10F THR* 4.3 0.8 + - - -
23F ILE* 3.6 1.7 - - - +
24F ALA* 3.6 2.4 - - - -
25F VAL* 2.9 45.5 + - + +
27F TYR* 3.7 31.0 - + + -
97F ARG 3.5 2.2 - - - -
98F MET* 3.6 22.2 - - + -
55G SER* 3.9 11.4 - - - +
56G PHE* 3.4 59.5 - + + +
57G SER 5.2 2.9 - - - -
58G LYS* 6.2 0.7 - - - -
63G TYR* 5.4 1.8 - - - -
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Residues in contact with PHE 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F TYR* 3.6 25.1 - + + -
8F PHE* 1.3 73.7 - - - +
10F THR* 1.3 60.5 + - - +
11F SER 4.3 0.2 - - - -
22F PHE* 3.4 34.8 - + + -
23F ILE 3.3 4.7 - - - -
24F ALA* 3.9 18.8 - - + -
25F VAL 5.8 0.4 - - - -
67F VAL* 4.7 5.2 - - + -
70F HIS* 3.6 29.6 - + + -
74F HIS* 4.1 12.1 - + + +
95F VAL 4.5 0.2 - - - -
96F GLN* 3.2 5.5 - - - -
97F ARG* 2.8 58.2 + - + +
99F TYR* 3.4 35.2 - + - -
56G PHE* 3.6 4.0 - - - -
2H ILE* 4.3 11.0 - - + -
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Residues in contact with THR 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PHE 5.2 0.5 + - - -
9F PHE* 1.3 70.4 - - - +
11F SER* 1.4 61.9 + - - +
12F VAL* 3.8 21.5 - - + -
22F PHE* 3.5 5.5 - - - -
23F ILE* 2.9 51.6 + - + +
94F THR* 3.9 6.5 - - + -
95F VAL 3.4 3.8 - - - -
96F GLN* 4.3 1.8 - - + -
33G SER* 4.6 0.2 - - - +
54G LEU* 4.4 10.1 + - + +
56G PHE* 3.3 25.5 - - - -
62G PHE* 3.6 30.3 - - + -
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Residues in contact with SER 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F PHE 4.3 0.2 - - - -
10F THR* 1.4 73.3 - - - +
12F VAL* 1.3 60.9 + - - +
20F PRO* 4.5 3.8 - - - +
21F ARG 3.2 9.7 + - - -
22F PHE* 4.2 11.6 - - - +
71F SER 5.1 1.0 + - - -
74F HIS* 4.0 30.0 + - - +
75F ARG* 4.7 0.7 + - - -
78F LEU* 3.4 25.8 - - - +
94F THR* 3.3 3.6 - - - -
95F VAL* 2.8 43.8 + - - -
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Residues in contact with VAL 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F THR* 3.8 17.7 - - + -
11F SER* 1.3 77.1 + - - +
13F SER* 1.3 65.6 + - - +
14F ARG* 3.8 4.9 - - - -
20F PRO* 3.3 4.2 - - - +
21F ARG* 2.8 45.4 + - + +
23F ILE* 4.8 6.5 - - + -
78F LEU* 4.3 0.2 - - - -
92F SER* 3.7 17.0 - - - +
93F HIS 3.4 10.1 - - - +
94F THR* 3.7 15.7 - - + +
32G PRO* 5.9 3.1 - - + -
33G SER* 3.6 23.8 - - - +
34G ASP* 5.2 8.7 - - - +
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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