Contacts of the strand formed by residues 2 - 11 (chain I) in PDB entry 2CHT
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3H ILE* 5.0 4.5 - - + -
40H GLU 4.1 6.5 - - - +
41H ASP 3.5 18.2 - - - +
43H VAL* 3.9 11.7 - - + +
96H GLN* 3.1 55.9 - - + +
3I ILE* 1.3 87.9 + - + +
4I ARG* 3.4 37.9 - - + +
96I GLN* 3.2 11.1 - - - +
97I THR 2.7 47.2 + - - +
98I ASP* 4.9 5.7 + - - +
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Residues in contact with ILE 3 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G MET* 4.2 12.1 - - - -
3G ILE* 4.5 14.6 - - + -
3H ILE* 4.0 28.5 - - + -
43H VAL* 3.5 17.5 - - + +
2I MET* 1.3 99.2 - - + +
4I ARG* 1.3 59.1 + - - +
43I VAL* 3.7 14.8 - - + -
94I THR* 3.6 28.0 - - + -
95I VAL 3.1 14.4 - - - +
96I GLN* 3.6 30.7 - - + +
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Residues in contact with ARG 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H GLU* 2.6 35.3 + - - +
42H VAL 4.1 5.1 + - - +
43H VAL* 3.7 9.4 - - - +
2I MET* 3.4 26.1 - - + +
3I ILE* 1.3 80.6 - - - +
5I GLY* 1.3 60.7 + - - +
94I THR* 4.5 0.2 - - - -
95I VAL* 2.7 37.5 + - - +
97I THR* 3.3 26.0 - - + +
99I VAL 3.7 20.3 + - - -
100I PRO* 4.8 2.6 - - - +
101I GLN* 2.7 49.7 + - - +
104I ILE* 3.9 17.0 - - + -
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Residues in contact with GLY 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H VAL 2.9 19.8 + - - -
44H GLN* 3.8 15.0 - - - -
72H PRO* 3.6 21.3 - - - +
4I ARG* 1.3 77.5 - - - +
6I ILE* 1.3 61.4 + - - +
92I MET* 4.4 1.6 - - - -
93I MET 3.2 9.4 - - - -
104I ILE* 3.9 8.0 - - - +
106I HIS* 3.7 8.0 + - - -
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Residues in contact with ILE 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ARG 5.1 0.2 - - - -
5I GLY* 1.3 76.9 - - - +
7I ARG* 1.3 67.5 + - - +
31I ILE* 3.6 27.7 - - + +
35I ASN* 3.9 25.4 - - + +
37I THR* 4.1 5.2 - - - +
91I VAL 3.6 1.4 - - - +
92I MET* 3.4 5.4 - - - -
93I MET* 2.8 40.9 + - + +
95I VAL* 3.7 38.1 - - + -
104I ILE* 3.8 15.3 - - + -
105I ARG 3.2 27.4 - - - +
106I HIS* 3.8 2.5 - - - -
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Residues in contact with ARG 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H PRO* 3.6 24.9 - - + -
73H VAL 3.2 23.7 + - - +
74H THR* 3.6 16.9 + - - -
6I ILE* 1.3 75.5 - - - +
8I GLY* 1.3 81.5 + - - +
9I ALA* 4.3 0.4 - - - +
31I ILE* 3.9 5.8 - - - +
90I ARG* 3.6 10.3 - - - +
91I VAL 3.2 14.0 + - - -
92I MET* 3.6 22.9 - - - -
106I HIS* 3.0 26.4 - - + +
107I VAL 3.0 21.0 + - - -
108I TYR* 3.1 22.0 + - - +
208I TSA 2.8 45.4 + - - +
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Residues in contact with GLY 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ARG* 1.3 95.1 + - - +
9I ALA* 1.3 59.4 + - - -
27I LEU* 3.9 0.9 - - - -
31I ILE* 3.8 7.0 - - - -
90I ARG* 3.4 0.5 - - - -
91I VAL* 3.1 37.9 + - - +
107I VAL 3.2 14.6 - - - -
108I TYR* 4.8 2.9 - - - -
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Residues in contact with ALA 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ARG* 4.3 0.2 - - - +
8I GLY* 1.3 76.6 - - - +
10I THR* 1.3 62.5 + - - +
27I LEU* 3.5 7.3 - - - +
88I CYS* 4.3 1.3 - - - -
89I ILE 3.2 9.6 - - - -
90I ARG* 4.1 15.3 - - + -
107I VAL 3.2 5.7 + - - +
108I TYR* 3.5 21.9 - - + -
109I LEU 2.8 25.1 + - - -
112I ALA* 3.6 17.0 - - + -
115I LEU* 4.1 5.2 - - + -
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Residues in contact with THR 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I ALA* 1.3 76.1 - - - +
11I THR* 1.3 64.7 + - - +
23I LYS* 4.1 30.7 + - + +
24I THR* 4.4 2.0 - - - +
27I LEU* 3.7 27.3 - - + +
88I CYS* 3.2 7.1 - - - -
89I ILE* 3.0 45.8 + - + +
109I LEU* 3.3 15.3 + - - +
110I GLU* 3.3 21.5 - - - +
112I ALA* 4.0 0.9 - - - -
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Residues in contact with THR 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I THR* 1.3 84.6 + - - +
12I VAL* 1.3 68.8 + - - +
13I GLU 4.3 0.3 + - - -
23I LYS* 4.4 6.4 + - - +
85I LEU* 3.7 24.7 - - + -
86I LYS 3.7 10.3 - - - +
87I LYS 3.2 6.5 - - - -
88I CYS* 3.6 21.5 - - + +
110I GLU* 3.4 19.0 - - - +
111I LYS* 2.9 38.4 + - + +
112I ALA 3.9 3.6 - - - +
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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