Contacts of the helix formed by residues 4 - 19 (chain 7) 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 LYS 4 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37 ALA* 1.3 89.3 - - - +
57 SER* 1.3 59.4 + - - +
67 ALA 3.2 1.6 - - - -
77 ALA* 3.2 12.0 + - + +
87 ASN* 2.9 36.0 + - - +
387 GLU* 3.5 25.8 - - - +
417 ARG* 3.5 23.9 - - - +
476B SER 4.6 7.9 - - - +
477B ASN* 5.6 1.6 - - - +
130Z THR* 5.2 11.0 - - + -
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Residues in contact with SER 5 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37 ALA* 4.7 4.5 - - - -
47 LYS* 1.3 80.4 + - - +
67 ALA* 1.3 58.7 + - - +
87 ASN* 4.1 7.5 - - - +
97 LYS* 2.8 31.9 + - - +
477B ASN* 4.4 20.0 + - - -
478B HIS* 5.5 10.5 - - - -
480B GLU* 5.7 4.0 + - - -
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Residues in contact with ALA 6 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37 ALA* 3.9 10.6 + - - +
47 LYS 3.2 0.6 - - - -
57 SER* 1.3 79.4 + - - +
77 ALA* 1.3 59.4 + - - +
97 LYS* 3.8 16.9 + - - +
107 LEU* 3.0 31.2 + - - +
126Z VAL* 5.4 0.4 - - - -
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Residues in contact with ALA 7 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37 ALA 4.6 1.5 + - - +
47 LYS* 3.2 13.2 + - - +
67 ALA* 1.3 78.3 - - - +
87 ASN* 1.3 61.6 + - - +
107 LEU* 3.4 4.5 + - - +
117 ASP* 2.9 27.4 + - - +
347 LYS* 5.0 4.8 + - - +
123Z LEU* 5.7 1.2 - - - +
126Z VAL* 3.6 32.3 - - + +
127Z SER* 5.5 1.6 - - - +
130Z THR* 3.8 23.6 - - + +
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Residues in contact with ASN 8 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47 LYS* 2.9 30.0 + - - +
57 SER* 4.1 4.0 - - - +
77 ALA* 1.3 75.5 - - - +
97 LYS* 1.3 60.4 + - - +
117 ASP* 3.2 6.6 + - - +
127 TRP* 2.9 44.4 + - + +
347 LYS* 3.1 27.9 - - - +
387 GLU* 4.3 7.1 + - - +
473B TYR* 5.5 0.4 - - - -
477B ASN* 2.8 47.8 + - + +
478B HIS* 6.3 0.7 - - - +
130Z THR* 6.1 0.3 - - - +
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Residues in contact with LYS 9 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57 SER 2.8 22.9 + - - +
67 ALA* 3.8 18.3 + - - +
87 ASN* 1.3 74.5 - - - +
107 LEU* 1.3 66.6 + - + +
127 TRP* 3.4 7.3 + - - +
137 ALA* 2.9 29.9 + - + +
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Residues in contact with LEU 10 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67 ALA 3.0 17.8 + - - +
77 ALA* 3.9 4.9 - - - +
97 LYS* 1.3 87.3 - - + +
117 ASP* 1.3 57.5 + - - +
137 ALA* 3.4 14.1 - - + +
147 LYS* 2.9 31.4 + - + +
119Z THR* 3.8 25.6 - - + +
122Z VAL* 4.8 10.3 - - + -
123Z LEU* 3.7 39.9 - - + +
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Residues in contact with ASP 11 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77 ALA 2.9 17.4 + - - +
87 ASN* 3.5 11.5 + - - +
97 LYS 3.2 0.4 - - - -
107 LEU* 1.3 78.5 - - - +
127 TRP* 1.3 60.8 + - + +
147 LYS* 3.2 4.9 + - - +
157 VAL* 2.8 33.2 + - - +
317 SER* 3.3 29.3 - - - -
347 LYS* 3.3 20.9 + - - +
123Z LEU* 4.3 18.0 - - + +
127Z SER* 6.3 0.2 - - - -
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Residues in contact with TRP 12 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87 ASN* 2.9 35.4 + - + +
97 LYS* 4.0 6.7 - - - +
117 ASP* 1.3 75.6 - - + +
137 ALA* 1.3 60.6 + - - +
157 VAL* 3.3 28.4 - - + +
167 ILE* 2.9 34.3 + - + +
473B TYR* 2.7 50.9 + + - -
478B HIS* 5.7 1.6 - - - -
505B SER* 3.1 38.4 - - - -
506B PHE* 3.7 15.7 - + - -
508B ALA* 5.3 0.9 - - + -
509B THR* 3.2 38.6 - - + -
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Residues in contact with ALA 13 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97 LYS* 2.9 21.6 + - + +
107 LEU* 3.4 22.0 - - + +
127 TRP* 1.3 76.1 - - - +
147 LYS* 1.3 57.9 + - + +
167 ILE* 3.2 16.9 - - + +
177 SER* 2.9 32.0 + - - -
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Residues in contact with LYS 14 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107 LEU* 2.9 23.6 + - + +
117 ASP* 3.2 7.8 + - - +
137 ALA* 1.3 74.4 - - + +
157 VAL* 1.3 53.5 + - - +
177 SER* 3.5 12.2 - - - +
187 SER* 2.5 44.8 + - - +
7U PRO* 5.4 2.6 - - + +
116Z VAL* 2.8 29.8 + - + +
119Z THR* 2.5 40.2 + - - -
120Z THR* 3.2 27.0 - - - +
123Z LEU* 3.7 29.4 - - + -
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Residues in contact with VAL 15 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117 ASP* 2.8 26.4 + - - +
127 TRP* 3.1 35.6 + - + +
147 LYS* 1.3 77.4 - - - +
167 ILE* 1.3 65.0 + - + +
177 SER 3.1 0.2 - - - -
187 SER* 3.0 6.6 + - - -
197 LEU* 3.0 36.7 + - + +
287 GLN* 6.4 2.5 - - + -
317 SER* 6.1 0.9 - - - +
508B ALA* 5.0 7.0 - - + +
509B THR* 3.8 26.5 - - + -
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Residues in contact with ILE 16 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127 TRP* 2.9 16.0 + - + +
137 ALA* 3.2 21.5 - - + +
157 VAL* 1.3 79.4 - - + +
177 SER* 1.3 59.0 + - - +
197 LEU* 3.7 17.7 - - + +
207 ARG* 3.5 21.8 + - - -
508B ALA* 5.7 7.2 - - + -
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Residues in contact with SER 17 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137 ALA 2.9 18.7 + - - -
147 LYS* 3.9 18.9 - - - +
157 VAL 3.1 0.2 - - - -
167 ILE* 1.3 78.3 + - - +
187 SER* 1.3 54.4 + - - +
197 LEU 3.2 5.4 - - - -
207 ARG* 3.2 30.8 + - - +
217 ILE* 4.4 3.1 + - - +
116Z VAL* 5.4 14.0 - - - +
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Residues in contact with SER 18 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147 LYS* 2.5 31.1 + - - +
157 VAL* 3.0 8.0 + - - -
177 SER* 1.3 69.9 - - - +
197 LEU* 1.3 62.1 + - - +
207 ARG 3.1 1.1 - - - -
217 ILE* 3.0 44.7 - - - +
227 THR* 4.7 1.4 - - - +
247 SER* 5.7 8.2 - - - -
277 THR* 5.5 6.6 - - - +
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Residues in contact with LEU 19 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157 VAL* 3.0 34.5 + - + +
167 ILE* 3.7 20.9 - - + +
187 SER* 1.3 76.4 - - - +
207 ARG* 1.3 90.8 + - - +
217 ILE 3.3 1.0 + - - -
227 THR* 3.5 23.1 - - + +
508B ALA* 6.2 3.4 - - + +
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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