Contacts of the helix formed by residues 9 - 24 (chain I) in PDB entry 6CP3
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 SER 9 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G ALA 4.7 0.7 + - - -
148G ASP* 2.6 40.7 + - - +
151G LEU* 5.1 11.0 - - - -
211G GLU* 3.3 23.5 - - - +
3I TRP* 4.3 0.9 - - - -
4I ARG* 5.3 4.5 - - - +
7I GLY 4.2 0.2 + - - -
8I ILE* 1.3 75.8 - - - +
10I TYR* 1.3 54.4 + - - +
11I ALA* 4.3 2.6 + - - +
12I ALA* 3.1 7.6 + - - +
13I TYR* 2.6 33.9 + - - +
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Residues in contact with TYR 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208G ASP* 3.6 41.5 - - + +
211G GLU* 2.6 20.6 + - - +
212G TYR* 4.3 9.9 - + + -
51H GLN* 4.2 15.0 - - + +
52H LEU 3.8 14.7 + - - -
53H LEU* 5.9 5.4 - - + -
73H GLY 3.1 20.8 + - - -
74H PHE* 3.6 23.6 - + - -
3I TRP* 3.7 24.7 - + + -
4I ARG* 5.3 1.2 - - - +
9I SER* 1.3 69.2 - - - +
11I ALA* 1.3 60.4 + - - +
13I TYR* 3.2 22.9 + + - +
14I LEU* 3.0 52.4 + - + +
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Residues in contact with ALA 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G PHE* 4.5 5.2 - - + -
144G ALA* 4.1 11.1 - - + +
147G ALA* 4.5 12.8 - - + -
211G GLU* 4.0 17.2 + - + +
212G TYR* 5.0 4.0 - - - -
215G ALA* 3.7 30.1 - - + -
9I SER* 3.4 4.0 + - - +
10I TYR* 1.3 81.0 - - - +
12I ALA* 1.3 57.5 + - - +
14I LEU* 3.4 6.6 + - - +
15I ASN* 2.9 27.3 + - - +
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Residues in contact with ALA 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G ALA 4.6 4.8 + - - +
145G LEU* 5.9 3.4 - - + -
148G ASP* 3.5 36.3 - - + +
122H GLU* 6.1 0.7 - - - +
8I ILE* 3.7 13.2 - - + -
9I SER* 3.1 11.4 + - - +
11I ALA* 1.3 76.7 - - - +
13I TYR* 1.3 59.7 + - - +
15I ASN* 3.5 9.4 - - - +
16I VAL* 2.9 35.1 + - + +
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Residues in contact with TYR 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H LEU* 4.7 12.9 - - + +
54H PRO* 4.5 19.4 - - + +
125H ILE* 3.6 36.6 - - + +
128H GLU* 4.1 13.1 + - - +
129H VAL* 5.7 3.2 - - + +
3I TRP* 3.4 67.8 + + + -
8I ILE* 4.1 5.3 - - + +
9I SER 2.6 17.8 + - - +
10I TYR* 3.2 16.4 + + - +
12I ALA* 1.3 71.4 - - - +
14I LEU* 1.3 77.5 + - + +
16I VAL* 3.3 7.1 + - - +
17I ALA* 3.0 25.1 + - + +
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Residues in contact with LEU 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G PHE* 5.2 1.1 - - + -
212G TYR* 4.3 12.8 - - + -
52H LEU 4.6 1.3 - - - +
54H PRO* 4.3 4.7 - - + -
71H SER 3.3 19.5 - - - +
72H GLY* 3.6 13.0 - - - +
73H GLY* 3.5 20.4 - - - +
88H ILE* 3.5 21.2 - - + +
10I TYR* 3.0 51.8 + - + +
11I ALA* 4.0 3.8 - - - +
13I TYR* 1.3 97.8 - - + +
15I ASN* 1.3 56.6 + - - +
17I ALA* 3.3 5.9 + - + +
18I ALA* 2.8 26.5 + - - +
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Residues in contact with ASN 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G PHE* 4.8 3.5 - - - -
141G GLN* 3.1 62.5 + - - +
144G ALA* 3.8 13.0 - - + +
145G LEU* 4.0 9.9 - - - +
88H ILE* 4.7 2.4 - - - +
11I ALA 2.9 17.8 + - - +
12I ALA* 3.2 11.0 + - - +
14I LEU* 1.3 74.3 - - - +
16I VAL* 1.3 61.4 + - + +
18I ALA* 3.1 10.8 + - - +
19I GLN* 2.9 30.4 + - - +
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Residues in contact with VAL 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H GLU* 3.8 48.0 - - + +
125H ILE* 4.0 14.1 - - + -
126H GLN* 3.5 32.8 + - + +
8I ILE* 5.4 2.0 - - + -
12I ALA* 2.9 21.8 + - + +
13I TYR* 3.7 6.1 - - - +
15I ASN* 1.3 75.8 - - + +
17I ALA* 1.3 58.0 + - - +
19I GLN* 3.4 10.4 + - - +
20I ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H PRO* 4.4 7.4 - - + -
71H SER* 3.6 27.9 - - - +
125H ILE* 4.9 1.5 - - + +
129H VAL* 4.4 23.8 - - + +
13I TYR* 3.0 13.9 + - + +
14I LEU* 3.4 11.9 - - + +
15I ASN 3.2 0.2 - - - -
16I VAL* 1.3 78.3 - - - +
18I ALA* 1.3 55.6 + - - +
20I ALA* 3.3 6.8 + - - +
21I ILE* 2.9 29.8 + - - +
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Residues in contact with ALA 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G PHE* 5.6 1.6 - - + -
71H SER* 4.6 1.3 - - - -
88H ILE* 3.8 26.5 - - + -
89H GLU* 4.0 17.9 - - - +
14I LEU 2.8 13.6 + - - +
15I ASN* 3.1 17.5 + - - +
17I ALA* 1.3 77.7 - - - +
19I GLN* 1.3 58.5 + - + +
21I ILE* 3.8 1.4 - - - +
22I ARG* 2.9 31.0 + - - +
37I ARG* 6.0 2.2 - - - -
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Residues in contact with GLN 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G GLN* 3.3 37.6 - - + +
126H GLN* 4.6 12.0 + - - +
15I ASN* 2.9 23.5 + - - +
16I VAL* 3.4 11.4 + - - +
18I ALA* 1.3 75.8 - - + +
20I ALA* 1.3 58.3 + - - +
22I ARG* 3.7 5.9 - - - +
23I SER* 2.8 30.5 + - - -
38I SER* 4.4 21.0 + - - +
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Residues in contact with ALA 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H LYS* 5.7 1.3 - - - +
126H GLN* 3.7 28.2 - - + +
129H VAL* 4.3 17.0 - - + -
130H LEU* 5.3 7.4 - - + +
133H LEU* 5.3 1.3 - - - +
16I VAL 2.9 18.2 + - - +
17I ALA* 3.6 7.6 - - - +
18I ALA 3.2 0.2 - - - -
19I GLN* 1.3 76.3 - - - +
21I ILE* 1.3 61.0 + - - +
23I SER* 3.8 4.7 - - - -
24I SER* 2.9 30.5 + - - -
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Residues in contact with ILE 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H PHE* 4.7 20.2 - - + -
71H SER* 4.9 2.0 - - - -
89H GLU* 4.2 23.3 - - + -
96H PHE* 3.2 28.9 - - + -
129H VAL* 5.2 1.5 - - + +
133H LEU* 5.5 5.4 - - + -
17I ALA 2.9 16.4 + - - +
18I ALA 4.0 2.5 - - - +
20I ALA* 1.3 76.2 - - - +
22I ARG* 1.3 56.7 + - - +
24I SER* 3.5 5.3 - - - +
25I LEU 3.2 13.3 + - - -
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Residues in contact with ARG 22 (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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89H GLU* 5.3 6.0 + - - +
96H PHE* 4.5 2.9 - - - -
18I ALA 2.9 19.9 + - - +
19I GLN* 3.7 6.3 - - - +
21I ILE* 1.3 75.9 - - - +
23I SER* 1.3 58.9 + - - +
25I LEU* 3.3 21.4 - - - +
30I GLN* 3.5 16.5 + - - +
34I VAL* 3.8 27.8 - - + +
37I ARG* 6.3 1.8 - - + -
38I SER* 5.6 7.6 - - - -
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Residues in contact with SER 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H ILE* 3.3 19.9 - - - +
105H LEU* 4.1 16.0 - - - +
109H LYS* 4.9 11.7 - - - -
126H GLN* 6.1 0.4 - - - -
19I GLN 2.8 20.1 + - - -
20I ALA* 3.3 6.9 + - - -
21I ILE 3.3 0.2 - - - -
22I ARG* 1.3 75.9 - - - +
24I SER* 1.3 56.4 + - - +
25I LEU* 3.1 7.4 + - - +
30I GLN* 5.0 5.7 - - - +
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Residues in contact with SER 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H PHE* 2.9 15.6 - - - +
97H SER* 3.7 10.3 - - - -
98H GLN 4.4 1.6 + - - -
101H ILE* 4.1 11.7 - - - -
102H LYS* 4.3 17.3 - - - -
130H LEU* 4.3 22.0 - - - -
133H LEU* 4.5 9.6 - - - -
20I ALA 2.9 17.0 + - - -
21I ILE* 3.5 6.6 - - - +
22I ARG 3.5 0.2 - - - -
23I SER* 1.3 73.2 - - - +
25I LEU* 1.3 61.1 + - - +
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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
------------------------------------------------------------
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