Contacts of the strand formed by residues 34 - 41 (chain L) in PDB entry 1NSK
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 ARG 34 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L LEU* 6.2 1.1 - - - -
32L GLY 5.1 3.1 - - - +
33L PHE* 1.3 72.1 - - - +
35L LEU* 1.3 62.8 + - - +
36L VAL* 3.1 13.2 + - - +
78L TRP* 3.4 6.6 - - - -
79L GLU* 2.6 74.8 + - + +
140L VAL 3.4 11.9 + - - -
141L ASP* 4.0 2.8 + - - +
142L TYR* 3.0 89.5 + - + +
143L LYS* 5.7 0.4 - - - +
144L SER* 4.0 26.8 - - - +
147L HIS* 5.7 6.7 - - - -
151L TYR* 6.4 1.8 - - + -
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Residues in contact with LEU 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L ILE* 5.5 1.3 - - + -
34L ARG* 1.3 69.6 - - - +
36L VAL* 1.3 60.1 + - - +
37L ALA 3.0 33.0 - - - +
38L MET* 3.8 26.9 - - + -
76L MET* 4.3 9.2 - - + -
77L VAL 3.5 8.5 - - - +
78L TRP* 3.3 31.9 - - + -
142L TYR* 2.7 32.3 + - - +
16R VAL* 5.9 1.3 - - + -
21R VAL* 5.2 11.0 - - + -
40R PHE* 3.1 40.3 - - + -
74R VAL* 4.9 2.9 - - + -
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Residues in contact with VAL 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L ARG* 4.6 7.0 - - - +
34L ARG* 3.6 14.1 - - - +
35L LEU* 1.3 74.3 - - - +
37L ALA* 1.3 58.2 + - - +
77L VAL* 2.8 20.6 + - + +
79L GLU* 3.5 39.9 - - + +
139L LEU* 3.6 33.9 - - + -
140L VAL* 2.8 52.5 + - - +
141L ASP* 4.4 6.1 - - - +
40R PHE* 3.6 2.6 - - - -
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Residues in contact with ALA 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L LEU* 3.0 10.8 - - - +
36L VAL* 1.3 79.6 - - - +
38L MET* 1.3 62.5 + - - +
76L MET* 3.1 1.8 - - - -
77L VAL* 2.9 27.9 + - + -
134L PHE* 4.0 14.4 - - + -
138L GLU* 3.2 23.6 - - + +
139L LEU* 3.4 23.1 - - + -
40R PHE* 3.9 7.2 - - - -
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Residues in contact with MET 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L ILE* 3.9 22.4 - - + -
35L LEU* 3.8 20.9 - - + -
37L ALA* 1.3 79.7 - - - +
39L LYS* 1.3 64.7 + - - +
74L VAL* 4.0 1.6 - - + -
75L ALA 3.2 7.0 - - - +
76L MET* 3.6 20.6 - - + +
134L PHE* 4.1 2.4 - - - -
21R VAL* 4.7 3.1 - - + -
38R MET* 3.5 46.2 - - + -
39R LYS* 3.4 3.4 - - - +
40R PHE* 3.0 38.8 + - + +
74R VAL* 3.7 31.0 - - + -
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Residues in contact with LYS 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L MET* 1.3 79.3 - - - +
40L PHE* 1.3 60.1 + - - +
41L LEU* 3.8 32.6 - - + +
74L VAL* 3.5 4.4 - - - +
75L ALA* 2.8 38.3 + - + -
133L TRP* 3.2 23.0 + - + +
134L PHE* 3.6 18.1 - - + +
135L LYS* 5.2 5.3 - - - +
138L GLU* 3.0 40.5 + - - -
38R MET* 3.4 8.5 - - - +
39R LYS* 4.5 4.7 - - + +
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Residues in contact with PHE 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L VAL* 4.0 14.6 - - + -
39L LYS* 1.3 73.0 - - - +
41L LEU* 1.3 64.1 + - - +
72L PRO* 3.4 33.0 - - + -
73L VAL 3.3 12.6 - - - -
74L VAL* 3.4 20.9 - - + +
35R LEU* 3.1 44.2 - - + -
36R VAL 3.5 19.7 - - - -
37R ALA* 3.8 8.7 - - - -
38R MET* 2.9 31.3 + - + +
138R GLU* 4.4 8.3 - - - +
140R VAL* 3.8 12.0 - - + +
142R TYR* 3.6 14.1 - + - -
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Residues in contact with LEU 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L LYS* 3.8 42.0 - - + +
40L PHE* 1.3 78.1 - - - +
42L ARG* 1.3 57.8 + - - +
43L ALA* 4.3 11.2 - - - +
47L HIS* 5.2 5.2 - - + +
72L PRO* 3.9 4.0 - - - -
73L VAL* 2.8 54.3 + - + +
75L ALA* 4.2 3.1 - - + -
133L TRP* 4.2 23.3 - - + +
140R VAL* 3.9 9.4 - - - -
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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