Contacts of the strand formed by residues 2 - 11 (chain L) in PDB entry 2CHS
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 MET 2 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3K ILE* 4.5 5.4 - - - -
40K GLU 3.8 6.3 - - - +
41K ASP* 3.6 26.7 - - - +
43K VAL* 3.9 10.1 - - + +
96K GLN* 3.7 39.9 - - + +
3L ILE* 1.3 88.1 + - - +
4L ARG* 3.6 41.3 - - - +
96L GLN* 3.5 11.3 - - - +
97L THR 2.9 40.7 + - - +
98L ASP* 4.8 7.1 + - - +
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Residues in contact with ILE 3 (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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2J MET* 4.4 11.4 - - + -
3J ILE* 4.7 14.6 - - + -
3K ILE* 4.2 22.2 - - + -
43K VAL* 3.2 33.4 - - + +
2L MET* 1.3 92.5 - - - +
4L ARG* 1.3 60.9 + - - +
43L VAL* 4.0 17.0 - - + -
94L THR* 3.5 29.2 - - + -
95L VAL 3.3 5.2 - - - +
96L GLN* 3.7 31.6 - - + -
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Residues in contact with ARG 4 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K GLU* 2.9 33.1 + - - +
42K VAL 3.7 5.3 + - - -
43K VAL* 3.7 11.7 - - - +
72K PRO* 5.8 0.7 - - + -
2L MET* 3.6 34.4 - - + +
3L ILE* 1.3 76.9 - - - +
5L GLY* 1.3 65.2 + - - +
93L MET 3.8 0.2 - - - +
94L THR* 3.5 1.9 - - - -
95L VAL* 2.9 33.7 + - + +
97L THR* 3.6 22.4 + - + +
99L VAL 3.6 14.2 + - - -
100L PRO* 5.1 2.0 - - - +
101L GLN* 3.4 55.5 + - - +
104L ILE* 4.2 14.4 - - + -
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Residues in contact with GLY 5 (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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43K VAL 3.0 13.1 + - - -
44K GLN* 3.7 10.8 - - - -
72K PRO* 3.4 21.4 - - - +
4L ARG* 1.3 77.4 - - - +
6L ILE* 1.3 64.6 + - - +
92L MET* 3.7 13.7 - - - -
93L MET 3.4 6.5 - - - -
104L ILE* 4.1 4.9 - - - +
106L HIS* 3.6 9.4 + - - -
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Residues in contact with ILE 6 (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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4L ARG 4.7 0.2 - - - +
5L GLY* 1.3 78.3 - - - +
7L ARG* 1.3 64.4 + - - +
31L ILE* 3.7 23.9 - - + +
35L ASN* 3.7 36.1 - - + +
37L THR* 4.4 1.1 - - - +
91L VAL* 3.7 2.3 - - - +
92L MET* 3.5 6.3 - - - +
93L MET* 2.8 62.3 + - + +
95L VAL* 3.8 24.2 - - + -
104L ILE* 3.8 17.0 - - + -
105L ARG 3.8 9.9 - - - +
106L HIS* 3.9 3.4 - - + -
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Residues in contact with ARG 7 (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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72K PRO* 4.1 13.9 - - + -
73K VAL 3.5 26.8 + - - +
74K THR* 4.2 16.6 + - - +
6L ILE* 1.3 78.0 - - - +
8L GLY* 1.3 83.0 + - - +
9L ALA* 3.7 5.3 - - - +
31L ILE* 4.3 5.1 - - - +
90L ARG* 3.6 24.9 - - - +
91L VAL 3.1 19.8 + - - +
92L MET* 3.7 24.0 - - + -
106L HIS* 3.1 25.3 - - + -
107L VAL 3.0 20.8 + - - -
108L TYR* 3.4 32.9 + - - +
115L LEU* 5.4 0.4 - - - +
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Residues in contact with GLY 8 (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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7L ARG* 1.3 93.5 + - - +
9L ALA* 1.3 59.4 + - - -
27L LEU* 4.1 2.2 - - - -
31L ILE* 4.1 8.5 - - - -
90L ARG* 3.4 0.2 - - - -
91L VAL* 3.1 37.5 + - - +
107L VAL 3.0 13.2 - - - -
108L TYR* 4.7 1.8 - - - -
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Residues in contact with ALA 9 (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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7L ARG* 3.7 12.1 - - - +
8L GLY* 1.3 74.6 - - - +
10L THR* 1.3 61.4 + - - +
27L LEU* 3.5 8.7 - - - +
88L CYS* 4.3 1.6 - - - -
89L ILE 3.2 12.1 - - - +
90L ARG* 4.0 6.3 - - + -
107L VAL 3.1 6.7 + - - -
108L TYR* 3.7 19.2 - - + -
109L LEU 2.9 24.3 + - - -
112L ALA* 3.7 11.9 - - + -
115L LEU* 3.8 10.1 - - + -
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Residues in contact with THR 10 (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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9L ALA* 1.3 75.5 - - - +
11L THR* 1.3 70.0 + - - +
23L LYS* 4.1 26.6 + - + +
24L THR 4.5 0.7 - - - +
27L LEU* 3.7 31.2 - - + -
88L CYS* 3.4 5.4 - - - -
89L ILE* 2.9 45.8 + - + +
109L LEU* 3.5 16.3 + - - +
110L GLU* 3.5 21.7 - - - +
112L ALA* 4.2 0.9 - - - -
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Residues in contact with THR 11 (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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10L THR* 1.3 85.0 + - - +
12L VAL* 1.3 70.9 + - - +
13L GLU* 5.3 0.3 + - - -
23L LYS* 3.9 9.9 - - - +
85L LEU* 3.5 33.7 - - + -
86L LYS 3.8 16.2 - - - +
87L LYS 3.1 9.2 - - - +
88L CYS* 4.1 1.3 - - - -
110L GLU* 3.5 12.2 - - - +
111L LYS* 3.0 36.9 + - + +
112L ALA 3.8 7.4 - - - +
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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