Contacts of the strand formed by residues 32 - 41 (chain C) in PDB entry 1I8F
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 32 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B LYS* 4.3 21.6 + - + +
28B LEU 4.7 2.6 + - - -
31B SER* 5.0 13.8 + - - -
74B LEU* 3.3 30.5 - - + +
75B PHE* 5.0 3.4 - + - -
26C VAL 4.7 0.2 - - - -
27C LYS* 3.3 7.8 - - - +
28C LEU* 3.0 49.1 + - + +
29C ARG 3.3 22.2 - - - -
30C ASP* 3.4 18.3 + - + +
31C SER* 1.3 78.8 + - - +
33C GLU* 1.3 61.2 + - - +
34C ILE* 4.9 5.2 - - + -
54C GLU* 4.4 11.9 + - - -
56C ILE* 6.1 1.8 - - - +
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 3.6 27.0 - - + +
26C VAL 3.7 3.1 - - - -
27C LYS* 3.7 29.9 + - + -
31C SER 3.9 3.0 + - - +
32C HIS* 1.3 74.2 - - - +
34C ILE* 1.3 66.7 + - - +
35C ARG* 5.2 2.9 + - - -
54C GLU* 3.6 2.6 - - - +
55C ILE* 2.9 67.7 + - + +
1005C GOL 5.4 0.3 + - - -
63D ARG* 4.2 11.4 + - - -
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 3.9 12.6 - - + -
25C LEU* 3.5 4.9 - - - +
26C VAL* 2.7 45.6 + - + +
28C LEU* 3.7 33.2 - - + -
32C HIS* 4.9 3.8 - - + -
33C GLU* 1.3 82.2 - - - +
35C ARG* 1.3 66.9 + - - +
49C LEU* 3.7 28.5 - - + -
52C ALA* 4.7 0.2 - - + -
53C GLU 3.3 13.9 - - - +
54C GLU* 4.4 11.7 - - + +
55C ILE* 4.1 1.3 - - - -
66C MET* 3.8 28.9 - - + -
68C VAL* 4.8 4.9 - - + -
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLN* 3.8 26.9 - - - +
24C VAL 3.2 11.0 - - - +
25C LEU* 3.8 15.5 - - + -
33C GLU* 5.2 3.8 + - - -
34C ILE* 1.3 80.7 - - - +
36C GLY* 1.3 56.3 + - - +
49C LEU* 4.6 0.7 - - - -
51C ASP 4.2 0.4 - - - +
52C ALA* 3.1 3.1 - - - +
53C GLU* 2.6 70.4 + - + +
55C ILE* 3.9 21.5 - - + +
60C VAL* 3.8 22.2 - - - +
79C VAL* 4.7 2.0 - - + -
1005C GOL 3.5 24.6 + - - +
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Residues in contact with GLY 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLN* 3.3 10.0 - - - +
24C VAL* 2.8 33.3 + - - +
35C ARG* 1.3 77.6 - - - +
37C ILE* 1.3 65.3 + - - -
49C LEU* 4.3 13.5 - - - +
50C GLU 3.7 8.3 - - - -
51C ASP 4.1 3.8 - - - -
52C ALA* 3.8 7.4 - - - -
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Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY* 3.7 25.1 - - - +
22C LYS 3.4 3.1 - - - -
23C GLN* 4.1 26.7 - - + +
36C GLY* 1.3 73.0 - - - -
38C LEU* 1.3 64.7 + - - +
39C ARG* 3.2 36.2 + - - +
49C LEU* 3.2 4.6 - - - -
50C GLU 2.8 39.9 + - - +
51C ASP* 4.2 19.7 - - + +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 3.6 41.5 - - + +
19C SER* 3.7 19.7 - - - +
20C ILE* 3.4 12.7 - - + -
21C GLY* 2.7 31.7 + - - -
22C LYS 2.9 13.0 + - - +
24C VAL* 4.2 14.8 - - + -
36C GLY 3.5 2.2 + - - -
37C ILE* 1.3 70.0 - - - +
39C ARG* 1.3 57.2 + - - +
40C SER 3.4 23.6 - - - +
41C PHE* 4.1 11.4 - - + -
47C LEU* 3.9 20.0 - - + -
48C LEU 3.8 6.5 - - - +
49C LEU* 3.8 13.9 - - + -
76C ILE* 5.9 0.4 - - + -
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ILE* 3.7 21.2 - - - +
21C GLY* 3.9 15.1 + - - +
37C ILE* 3.6 34.9 - - - +
38C LEU* 1.3 76.8 - - - +
40C SER* 1.3 65.6 + - - +
48C LEU* 2.8 27.8 + - + +
50C GLU* 2.6 48.9 + - + +
51C ASP* 4.8 6.1 + - - -
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA* 2.7 35.5 + - - -
11B THR* 3.3 10.0 - - - +
20C ILE* 4.1 7.8 - - - +
38C LEU* 3.4 8.7 - - - +
39C ARG* 1.3 81.9 - - - +
41C PHE* 1.3 67.4 + - - +
47C LEU* 3.5 0.3 - - - -
48C LEU* 2.9 37.3 + - - +
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Residues in contact with PHE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA* 5.7 1.6 - - - +
11B THR* 3.3 11.8 - - - +
14C ALA 5.7 4.3 - - - -
16C LEU* 3.5 30.1 - - + -
17C GLN* 3.4 55.9 - - + -
20C ILE* 3.7 17.7 - - + -
38C LEU* 4.1 4.0 - - + -
40C SER* 1.3 79.4 - - - +
42C ASP* 1.3 73.1 + - - +
45C VAL 5.5 0.2 - - - -
46C ASN 3.2 15.3 - - - +
47C LEU* 3.9 14.1 - - + -
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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