Contacts of the strand formed by residues 33 - 39 (chain C) in PDB entry 3NIF
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 33 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C PHE* 3.9 28.5 - - + -
26C HIS 3.4 6.1 - - - +
27C LYS* 3.8 30.5 - - + -
31C GLY 3.4 7.6 + - - +
32C ARG* 1.3 78.6 - - - +
34C ALA* 1.3 72.8 + - - +
35C ILE* 5.9 0.7 - - + -
58C TRP* 3.7 22.7 + - + +
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Residues in contact with ALA 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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25C PHE* 3.5 5.0 - - - -
26C HIS* 2.7 36.3 + - + +
32C ARG 3.7 2.2 + - - +
33C VAL* 1.3 78.6 - - - +
35C ILE* 1.3 66.4 + - - +
55C LEU* 4.3 18.8 - - + -
56C CYS 3.3 18.2 - - - +
57C PRO* 4.1 6.7 - - + -
58C TRP* 4.5 3.4 - - - +
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Residues in contact with ILE 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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11C TYR* 3.9 33.4 - - + +
23C LEU* 4.6 11.7 - - + -
24C ASP 3.5 10.3 - - - +
25C PHE* 4.8 18.4 - - + -
33C VAL* 5.9 0.4 - - + -
34C ALA* 1.3 78.1 - - - +
36C VAL* 1.3 66.1 + - - +
37C VAL* 3.6 22.0 + - + -
55C LEU* 3.6 3.6 - - - -
56C CYS* 2.7 48.1 + - + +
58C TRP* 5.2 10.8 - - + +
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Residues in contact with VAL 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 LEU* 3.1 8.4 - - - +
24C ASP* 2.8 44.0 + - + +
26C HIS* 3.4 30.3 - - + -
35C ILE* 1.3 72.1 - - - +
37C VAL* 1.3 61.1 + - - +
53C VAL* 3.8 19.5 - - + -
54C PHE 3.5 4.0 - - - +
55C LEU* 4.3 2.7 - - + -
97C VAL* 4.2 14.6 - - + -
98C VAL 5.6 0.2 - - - -
99C SER* 4.4 9.0 - - - +
104C ILE* 3.7 43.1 - - + -
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Residues in contact with VAL 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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11C TYR* 5.9 1.1 - - + -
19C PHE* 3.8 30.3 - - + -
20C GLY* 3.2 37.0 - - - +
22C SER 3.7 4.3 - - - +
23C LEU* 4.6 6.5 - - + -
35C ILE* 3.6 19.3 - - + -
36C VAL* 1.3 80.1 - - - +
38C GLY* 1.3 61.7 + - - +
53C VAL* 3.5 2.8 - - - +
54C PHE* 2.8 43.4 + - + +
56C CYS* 4.0 19.5 - - - -
97C VAL* 4.6 3.1 - - - -
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Residues in contact with GLY 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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20C GLY 3.0 23.2 + - - -
21C PHE 3.4 10.2 + - - -
22C SER* 2.9 16.5 + - - -
37C VAL* 1.3 72.6 - - - +
39C ALA* 1.3 59.0 + - - -
40C PRO* 3.8 0.7 - - - -
52C GLY 3.9 2.0 - - - -
53C VAL* 4.7 0.4 - - - -
94C GLY* 3.3 31.4 - - - -
97C VAL* 3.9 7.2 - - - +
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Residues in contact with ALA 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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17C SER* 3.0 17.9 - - - +
18C GLN 3.7 2.0 - - - -
19C PHE* 3.5 17.0 - - + -
37C VAL 4.0 0.2 + - - -
38C GLY* 1.3 72.6 - - - -
40C PRO* 1.3 60.8 - - - +
41C ARG 3.0 4.3 + - - -
42C THR* 2.6 36.5 + - - +
52C GLY 2.9 21.1 + - - +
54C PHE* 3.8 21.3 - - + -
94C GLY 3.9 0.6 + - - -
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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