Contacts of the strand formed by residues 11 - 19 (chain C) in PDB entry 3ISW
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 VAL 11 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2275A VAL 3.4 2.6 - - - +
2276A GLU* 3.3 5.5 - - - +
2277A GLY 2.9 39.5 + - - +
2278A PRO 3.7 7.2 - - - +
2279A SER* 3.6 23.8 - - - +
2280A LYS* 3.7 27.8 - - + +
10C SER* 1.3 74.7 - - - +
12C VAL* 1.3 65.1 + - - +
13C SER* 4.4 4.0 - - - +
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Residues in contact with VAL 12 (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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2274A ALA* 4.7 9.2 - - + -
2275A VAL 3.6 5.2 - - - +
2276A GLU* 3.7 23.8 - - + +
10C SER* 3.8 10.7 + - - +
11C VAL* 1.3 83.4 - - - +
13C SER* 1.3 62.3 + - - +
14C LYS* 4.0 30.8 + - + +
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Residues in contact with SER 13 (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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2274A ALA* 3.3 4.7 - - - -
2275A VAL* 3.0 33.1 + - - -
2279A SER 4.7 0.2 + - - -
2280A LYS* 3.5 11.4 - - - +
2281A ALA* 2.8 52.6 + - - +
2283A ILE* 3.6 8.7 - - - +
11C VAL* 4.4 1.9 - - - +
12C VAL* 1.3 73.2 - - - +
14C LYS* 1.3 60.6 + - - +
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Residues in contact with LYS 14 (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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2272A ALA* 6.3 0.7 - - + -
2273A ILE 3.3 9.6 - - - +
2274A ALA* 4.1 13.7 - - + -
2283A ILE* 4.3 4.1 - - - +
2278B PRO* 4.7 9.9 - - - +
12C VAL* 4.0 23.5 + - + +
13C SER* 1.3 79.1 - - - +
15C LEU* 1.3 63.1 + - - +
16C PHE* 3.6 33.7 - - + -
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Residues in contact with LEU 15 (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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2273A ILE* 3.0 31.4 + - + +
2283A ILE* 3.6 30.2 - - + +
2284A SER* 3.6 25.4 - - - -
2285A PHE* 3.3 30.8 - - + -
2276B GLU* 3.7 20.6 - - + +
2277B GLY* 3.6 17.9 - - - +
14C LYS* 1.3 74.7 - - - +
16C PHE* 1.3 91.2 + - - +
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Residues in contact with PHE 16 (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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2271A LEU 3.4 8.3 - - - +
2272A ALA* 3.7 26.9 - - + -
2273A ILE 5.8 0.2 - - - -
2285A PHE* 4.1 2.5 - - - -
2275B VAL 4.5 0.7 - - - -
2276B GLU* 3.5 3.3 - - - +
2277B GLY 3.0 34.4 + - - +
2278B PRO 3.6 15.9 - - - -
2279B SER* 3.4 30.3 - - - +
2280B LYS* 3.7 29.4 - - + +
14C LYS* 3.6 43.3 - - + -
15C LEU* 1.3 83.7 - - - +
17C PHE* 1.3 64.4 + - - +
18C SER* 4.2 0.4 - - - +
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Residues in contact with PHE 17 (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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2271A LEU* 2.9 34.9 + - + -
2285A PHE* 3.6 35.4 - + + -
2287A ASP* 3.8 33.2 - - + -
2293A CYS* 5.3 7.4 - - - -
2274B ALA* 3.5 24.5 - - + -
2275B VAL 3.6 3.1 - - - -
2276B GLU* 3.8 35.0 - - + -
2308B SER* 5.4 2.2 - - - -
16C PHE* 1.3 75.3 - - - +
18C SER* 1.3 59.3 + - - +
19C TRP* 3.3 39.5 - + + -
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Residues in contact with SER 18 (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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2269A GLY 3.3 10.8 - - - -
2270A GLY* 4.0 6.2 - - - -
2274B ALA* 3.2 3.0 - - - +
2275B VAL 2.7 34.6 + - - -
2279B SER 4.8 0.9 + - - -
2280B LYS* 3.8 11.1 - - - +
2281B ALA* 3.0 47.9 + - - +
2283B ILE* 3.9 6.2 - - - +
16C PHE* 5.1 0.2 - - - +
17C PHE* 1.3 77.7 + - - +
19C TRP* 1.3 60.1 + - - +
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Residues in contact with TRP 19 (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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2263A THR* 3.8 20.9 - - + -
2267A GLY 3.1 31.1 + - - -
2268A ALA* 3.6 4.4 - - - +
2269A GLY* 3.1 37.4 + - - +
2271A LEU* 3.2 36.8 - - + -
2293A CYS* 6.4 0.2 - - - -
2311A PHE* 3.6 20.0 - + - -
2272B ALA* 6.1 2.2 - - + -
2273B ILE 3.2 14.6 - - - +
2274B ALA* 3.7 13.2 - - + -
2283B ILE* 4.3 7.5 - - - +
17C PHE* 3.3 38.6 - + + -
18C SER* 1.3 74.2 - - - +
20C THR* 1.3 86.2 + - - +
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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