Contacts of the helix formed by residues 826 - 837 (chain C) in PDB entry 1P3A
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 PRO 826 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818C SER* 3.4 6.1 - - - +
824C GLN 3.8 1.0 - - - -
825C PHE* 1.3 90.5 - - + +
827C VAL* 1.3 65.6 + - - +
828C GLY 3.2 1.6 - - - +
829C ARG* 3.5 29.2 - - + +
830C VAL* 3.0 25.6 + - + +
852C ALA* 4.8 0.2 - - - -
1234D TYR* 4.3 10.8 - - + -
1237D TYR* 3.5 46.4 - - + +
30I A 5.1 2.0 - - - +
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Residues in contact with VAL 827 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817C ARG* 3.8 35.0 - - + +
818C SER* 2.9 32.5 + - - +
821C ALA* 4.7 0.2 - - + -
823C LEU* 4.3 15.7 - - + -
825C PHE 3.2 5.3 + - - +
826C PRO* 1.3 71.2 - - - +
828C GLY* 1.3 62.9 + - - +
830C VAL* 3.5 4.9 + - - -
831C HIS* 3.1 22.9 + - - +
848C PRO* 3.8 5.1 - - + +
849C VAL* 3.5 43.5 - - + +
852C ALA* 4.6 4.7 - - + -
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Residues in contact with GLY 828 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817C ARG* 3.8 16.8 + - - +
818C SER* 4.7 1.2 + - - -
826C PRO* 3.2 1.2 - - - +
827C VAL* 1.3 78.3 - - - +
829C ARG* 1.3 57.4 + - - +
831C HIS* 3.3 4.3 - - - +
832C ARG* 3.1 21.3 + - - +
30I A 3.3 26.6 + - - -
31I G 4.1 17.4 + - - -
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Residues in contact with ARG 829 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826C PRO* 3.2 27.0 + - + +
828C GLY* 1.3 73.0 - - - +
830C VAL* 1.3 63.7 + - - +
831C HIS 2.9 5.2 - - - -
832C ARG* 3.0 31.8 + - - +
833C LEU* 3.0 34.1 + - + +
1232D GLU* 3.3 29.7 + - - +
1233D SER 2.6 30.1 + - - +
1234D TYR* 4.9 7.4 - - - +
1237D TYR* 3.5 22.2 + - - -
29I A 5.2 1.0 + - - -
30I A 3.4 23.7 + - - +
267J G 3.7 23.6 + - - -
268J G 2.7 17.7 + - - -
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Residues in contact with VAL 830 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825C PHE* 5.5 0.7 - - + -
826C PRO* 3.0 26.7 + - + +
827C VAL 4.0 3.8 - - - +
829C ARG* 1.3 76.2 - - - +
831C HIS* 1.3 55.8 + - - +
833C LEU* 4.6 2.9 - - - -
834C LEU* 3.3 25.8 + - - +
848C PRO* 3.8 22.4 - - + +
851C LEU* 3.5 32.8 - - + -
852C ALA* 4.0 15.7 - - + +
855C LEU* 4.3 8.5 - - + -
1234D TYR* 3.9 21.3 - - + +
1267D PHE* 3.7 10.8 - - + -
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Residues in contact with HIS 831 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817C ARG* 3.0 37.9 + - - +
827C VAL 3.1 16.3 + - - +
828C GLY 3.3 7.0 - - - +
829C ARG 2.9 0.2 - - - -
830C VAL* 1.3 79.0 - - - +
832C ARG* 1.3 65.5 + - - +
834C LEU* 3.2 10.5 + - - +
835C ARG* 2.8 49.9 + - - +
843C VAL* 3.7 28.1 + - + +
844C GLY 4.0 10.5 + - - -
845C ALA* 4.9 1.8 - - - -
848C PRO* 3.4 18.2 - - + -
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Residues in contact with ARG 832 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828C GLY 3.1 7.6 + - - +
829C ARG* 3.0 23.8 + - - +
831C HIS* 1.3 74.0 - - - +
833C LEU* 1.3 75.8 + - - +
835C ARG* 2.6 35.0 + - - +
836C LYS* 3.0 22.4 + - - +
1232D GLU* 2.5 46.7 + - - -
29I A 3.2 40.3 + - - -
30I A 2.6 27.5 + - - +
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Residues in contact with LEU 833 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829C ARG* 3.0 30.2 + - + +
830C VAL* 4.3 1.8 - - - +
832C ARG* 1.3 95.1 - - - +
834C LEU* 1.3 61.5 + - - +
836C LYS* 3.5 31.1 - - + +
837C GLY* 3.0 22.3 + - - -
839C TYR* 3.9 4.0 - - - -
1232D GLU* 4.4 4.0 - - - +
1234D TYR* 3.7 26.7 - - + +
1264D ASN* 5.2 4.7 - - - +
1267D PHE* 3.8 23.5 - - + -
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Residues in contact with LEU 834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830C VAL 3.3 21.2 + - - +
831C HIS 3.2 8.0 + - - +
832C ARG 3.0 1.8 - - - -
833C LEU* 1.3 78.6 - - - +
835C ARG* 1.3 59.5 + - - +
837C GLY 4.1 1.3 - - - -
839C TYR* 3.7 43.3 + - + +
840C ALA 5.4 1.7 + - - +
843C VAL* 3.8 37.8 - - + +
847C ALA* 4.2 15.0 - - + -
848C PRO* 4.4 7.0 - - + -
851C LEU* 4.3 16.6 - - + -
1267D PHE* 4.0 15.7 - - + -
1271D ALA* 4.2 12.6 - - + -
1286D ILE* 5.0 8.9 - - + +
1291D ILE* 4.7 8.5 - - + -
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Residues in contact with ARG 835 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831C HIS* 2.8 49.5 + - - +
832C ARG* 2.6 20.3 + - - +
834C LEU* 1.3 74.0 - - - +
836C LYS* 1.3 61.1 + - - +
837C GLY 3.1 4.0 - - - -
838C ASN* 3.2 21.1 + - - +
841C GLU 5.8 0.6 + - - -
842C ARG* 5.7 0.2 - - - +
843C VAL* 4.4 12.8 - - + +
1041G GLU* 5.1 1.0 - - - +
258J T 3.3 40.3 + - - -
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Residues in contact with LYS 836 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832C ARG* 3.0 18.8 + - - +
833C LEU* 3.5 36.4 - - + +
835C ARG* 1.3 75.5 - - - +
837C GLY* 1.3 61.2 + - - +
838C ASN* 3.1 4.6 + - - +
1232D GLU* 5.0 2.4 + - - -
1479H HIS* 2.8 26.9 - - + +
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Residues in contact with GLY 837 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833C LEU 3.0 10.7 + - - -
835C ARG 3.1 0.6 - - - -
836C LYS* 1.3 79.5 - - - +
838C ASN* 1.3 72.8 + - - +
839C TYR* 3.3 39.1 - - - -
1479H HIS* 3.6 14.8 + - - -
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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