Contacts of the helix formed by residues 1101 - 1107 (chain C) in PDB entry 5NSS
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 LEU1101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806C PRO* 6.1 0.2 - - + -
1099C ASN* 2.9 15.8 + - - +
1100C PRO* 1.3 80.6 - - + +
1102C GLY* 1.3 57.0 + - - +
1104C PRO* 3.2 3.8 - - - +
1105C SER* 2.9 29.9 + - - -
504D GLN* 3.4 53.4 - - + +
505D ASP* 3.2 24.9 - - - +
508D LEU* 3.7 23.6 - - + -
725D MET* 3.5 38.5 - - + +
730D ALA* 4.7 3.8 - - + -
731D ARG* 4.7 0.4 - - + -
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Residues in contact with GLY1102 (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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813C GLU 5.8 2.2 - - - -
1099C ASN* 3.4 13.1 + - - -
1100C PRO 3.1 1.8 - - - -
1101C LEU* 1.3 77.0 - - - +
1103C VAL* 1.3 60.0 + - - +
1105C SER* 4.0 9.0 - - - -
1106C ARG* 2.9 40.9 + - - +
1107C MET 3.8 0.7 + - - -
1108C ASN* 4.3 5.1 + - - +
1111C GLN* 5.9 0.4 - - - -
504D GLN* 5.5 0.6 - - - +
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Residues in contact with VAL1103 (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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804C PHE* 5.1 5.8 - - + -
1099C ASN 4.6 1.5 + - - +
1100C PRO* 3.5 15.5 - - + +
1101C LEU 3.1 1.0 - - - -
1102C GLY* 1.3 75.9 - - - +
1104C PRO* 1.3 68.9 - - + +
1107C MET* 3.0 23.0 + - - -
1108C ASN* 3.1 35.0 + - + +
1109C ILE* 5.0 6.3 - - + -
1111C GLN* 4.0 24.0 - - + +
1112C ILE* 3.6 27.1 - - + -
639D VAL* 4.1 15.3 - - + -
740D LEU* 4.9 3.5 - - + +
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Residues in contact with PRO1104 (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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1100C PRO 3.2 12.3 - - - +
1101C LEU 3.2 14.4 - - - +
1103C VAL* 1.3 89.8 - - + +
1105C SER* 1.3 65.1 + - - +
1107C MET* 3.6 5.9 + - - +
639D VAL* 4.6 11.4 - - + -
722D ILE* 5.0 11.7 - - + -
725D MET* 3.5 31.9 - - + -
732D GLY* 4.6 6.9 - - - -
736D GLN* 3.5 19.4 - - - +
737D ILE* 5.5 5.8 - - + -
740D LEU* 4.4 25.7 - - + +
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Residues in contact with SER1105 (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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1101C LEU 2.9 19.6 + - - -
1102C GLY* 4.0 6.3 - - - -
1104C PRO* 1.3 80.1 - - - +
1106C ARG* 1.3 66.5 + - - +
1107C MET* 3.6 0.5 + - - +
504D GLN* 5.5 2.1 + - - -
725D MET* 4.6 0.2 - - - +
731D ARG* 4.1 19.5 - - - +
732D GLY 4.5 5.9 + - - +
736D GLN* 3.5 26.3 + - - -
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Residues in contact with ARG1106 (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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678C ARG* 3.2 61.7 + - + +
813C GLU* 4.9 8.0 + - - +
814C ASP* 2.8 47.6 + - - +
1071C GLY 5.3 1.2 + - - -
1072C ASN* 4.7 14.1 - - - +
1073C LYS 4.9 0.2 - - - +
1102C GLY* 2.9 24.4 + - - +
1105C SER* 1.3 80.4 - - - +
1107C MET* 1.3 71.5 + - - +
1108C ASN* 3.4 4.0 - - + +
460D ASP* 5.6 5.5 + - - +
461D PHE 5.9 0.4 - - - +
462D ASP* 3.2 27.1 + - - -
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Residues in contact with MET1107 (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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674C ASP* 4.1 0.9 - - - +
675C ASP* 3.3 50.4 + - + +
678C ARG* 4.2 1.9 - - - +
1103C VAL 3.0 12.6 + - - -
1104C PRO 3.6 4.9 + - - +
1105C SER 3.3 4.1 - - - +
1106C ARG* 1.3 81.5 - - - +
1108C ASN* 1.3 59.7 + - - +
1109C ILE* 3.9 4.2 + - + +
736D GLN* 4.1 26.7 - - + +
739D GLN* 3.7 26.9 - - + -
740D LEU* 4.5 7.0 - - + -
744D ARG* 5.4 0.4 - - - -
763D PHE* 3.5 29.4 - - + -
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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