Contacts of the helix formed by residues 826 - 838 (chain C) in PDB entry 1U35
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* 3.5 6.1 - - - +
824C ILE 3.5 0.4 - - - +
825C PHE* 1.3 84.1 - - + +
827C VAL* 1.3 65.0 + - - +
828C GLY 3.4 2.0 - - - -
829C ARG* 3.5 28.5 - - + +
830C MET* 3.1 37.9 + - + +
1234D TYR* 4.3 4.7 - - + -
1237D TYR* 3.3 52.9 - - + +
266J G 4.5 3.8 - - - +
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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 20.9 - - + +
818C SER* 3.0 41.0 + - - +
821C ALA* 5.0 2.0 - - + -
823C VAL* 3.6 17.5 - - + -
825C PHE 3.1 1.1 + - - +
826C PRO* 1.3 70.3 - - - +
828C GLY* 1.3 64.9 + - - +
830C MET* 3.2 2.3 + - - +
831C LEU* 3.1 16.3 + - - +
848C PRO* 3.5 13.6 - - + +
849C VAL* 3.6 40.8 - - + +
852C ALA* 4.3 12.8 - - + -
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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* 4.9 4.7 - - - -
826C PRO 3.4 0.4 - - - -
827C VAL* 1.3 74.8 - - - +
829C ARG* 1.3 64.7 + - - +
830C MET 2.9 4.7 - - - -
831C LEU* 2.9 21.5 + - - +
832C ARG* 3.1 11.6 + - - +
29I A 3.5 20.7 - - - +
30I A 3.9 21.5 + - - -
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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* 3.4 28.9 + - + +
828C GLY* 1.3 76.0 - - - +
830C MET* 1.3 58.8 + - + +
832C ARG* 3.5 2.6 - - - +
833C TYR* 3.2 55.7 + - + -
1230D ARG* 4.7 1.0 - - - +
1232D GLU* 3.3 26.8 + - - -
1233D SER 2.4 34.1 + - - +
1234D TYR* 5.2 3.0 - - + -
1237D TYR* 3.4 25.9 + - - -
29I A 3.5 30.9 + - - +
266J G 3.3 22.6 + - - -
267J T 3.1 13.2 + - - -
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Residues in contact with MET 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* 3.4 41.7 - - + -
826C PRO* 3.1 32.2 + - + +
827C VAL 3.6 4.7 - - - +
828C GLY 2.9 0.6 - - - -
829C ARG* 1.3 79.6 - - + +
831C LEU* 1.3 63.0 + - - +
832C ARG 3.1 1.3 - - - -
833C TYR* 3.6 6.0 - - + +
834C ILE* 2.8 32.4 + - - +
848C PRO* 4.1 10.8 - - + +
851C MET* 4.4 2.0 - - + -
852C ALA* 3.5 25.4 - - + -
855C LEU* 4.8 4.3 - - - -
1234D TYR* 4.0 23.6 - - + +
1267D PHE* 4.1 21.3 - - + -
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Residues in contact with LEU 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* 3.7 34.3 - - - +
827C VAL 3.1 7.2 + - - +
828C GLY* 2.9 12.4 + - - +
830C MET* 1.3 77.1 - - - +
832C ARG* 1.3 62.0 + - - +
834C ILE* 3.2 4.5 + - - +
835C LYS* 3.1 54.4 + - - +
843C ILE* 3.4 43.1 - - + +
844C GLY 5.0 0.2 - - - +
845C VAL* 5.8 2.0 - - + -
848C PRO* 3.5 22.6 - - + +
257J A 5.1 0.7 - - - +
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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 6.1 + - - +
829C ARG* 3.5 8.6 - - - +
831C LEU* 1.3 80.5 - - - +
833C TYR* 1.3 82.7 + - + +
835C LYS* 3.2 9.4 + - + +
836C LYS* 2.8 31.7 + - + +
1232D GLU* 2.3 35.2 + - - -
28I A 3.2 38.0 + - - -
29I A 2.2 48.9 + - - +
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Residues in contact with TYR 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* 3.2 34.1 + - + +
830C MET* 3.3 4.0 + - - +
832C ARG* 1.3 107.2 - - + +
834C ILE* 1.3 64.4 + - - +
836C LYS* 3.4 38.6 + - + +
837C GLY* 3.4 5.0 + - - -
838C HIS* 5.7 0.2 + - - -
1232D GLU* 2.5 33.7 + - - +
1233D SER 5.2 0.2 + - - -
1234D TYR* 3.7 31.4 - + - -
1264D ASN* 5.2 5.4 - - - -
1267D PHE* 3.6 26.6 - + + -
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Residues in contact with ILE 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 MET 2.8 26.4 + - - +
831C LEU* 3.5 6.1 - - - +
833C TYR* 1.3 76.4 - - - +
835C LYS* 1.3 59.2 + - - +
837C GLY 3.3 0.9 + - - -
838C HIS* 2.8 48.2 + - + +
843C ILE* 3.7 36.3 - - + -
847C ALA* 4.4 2.9 - - + -
848C PRO* 3.7 31.2 - - + -
851C MET* 3.7 21.3 - - + -
1267D PHE* 3.8 17.7 - - + -
1271D ALA* 5.2 3.1 - - + -
1286D ILE* 4.9 9.4 - - + -
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Residues in contact with LYS 835 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831C LEU* 3.1 47.6 + - + +
832C ARG* 3.2 8.9 + - + +
834C ILE* 1.3 71.6 - - - +
836C LYS* 1.3 51.3 + - - +
837C GLY 2.3 8.9 + - - -
838C HIS 2.9 2.0 + - - -
839C PRO* 2.3 47.9 - - + +
841C TYR 5.6 1.8 - - - +
843C ILE* 3.8 15.7 - - + -
257J A 3.3 33.7 + - - +
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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* 2.8 20.0 + - + +
833C TYR* 3.4 40.3 + - + +
835C LYS* 1.3 70.3 - - - +
837C GLY* 1.3 55.9 + - - +
839C PRO* 3.5 6.1 - - - -
1267D PHE* 5.1 6.7 - - - -
1040G LYS* 2.6 25.1 + - - -
1479H HIS* 3.5 33.6 + - + -
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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 TYR 3.4 10.1 + - - -
834C ILE 3.3 4.5 + - - -
835C LYS 2.3 14.1 + - - -
836C LYS* 1.3 78.3 - - - +
838C HIS* 1.3 70.8 + - - -
839C PRO* 3.0 8.5 - - - +
1040G LYS* 3.4 11.3 - - - -
1041G TYR* 5.7 0.2 - - - -
1479H HIS* 4.5 6.8 + - - -
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Residues in contact with HIS 838 (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 TYR 5.7 0.4 + - - -
834C ILE* 2.8 42.1 + - + +
835C LYS* 3.8 2.7 - - - -
837C GLY* 1.3 80.8 + - - -
839C PRO* 1.3 70.6 - - - +
840C LYS* 3.0 4.1 + - - -
841C TYR* 3.3 34.9 + - + +
843C ILE* 5.4 2.5 - - + +
1268D GLU* 5.6 0.2 - - - -
1271D ALA* 3.1 45.4 + - + +
1272D SER* 4.0 14.4 - - - -
1275D SER* 3.9 17.3 + - - -
1286D ILE* 5.2 6.1 - - + -
1040G LYS* 4.8 0.7 - - - +
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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