Contacts of the strand formed by residues 104 - 108 (chain C) in PDB entry 1R1P
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 VAL 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C GLU* 3.7 33.9 - - + +
74C LEU* 3.7 30.1 - - + -
75C MET* 3.8 17.1 - - + +
97C SER* 4.0 15.9 - - - -
98C VAL 3.5 22.4 - - - +
99C ARG* 4.1 4.9 - - - -
103C ASP* 1.3 81.1 - - - +
105C GLN* 1.3 67.1 + - - +
106C HIS* 3.8 20.6 + - + -
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Residues in contact with GLN 105 (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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96C ILE 3.7 0.9 - - - +
97C SER* 3.4 1.7 - - - -
98C VAL* 2.8 35.0 + - - +
100C HIS* 3.7 36.2 + - + +
103C ASP* 2.7 32.9 + - - +
104C VAL* 1.3 76.9 - - - +
106C HIS* 1.3 66.7 + - - +
107C PHE* 4.2 2.0 - - - -
143C LYS* 4.2 12.6 - - - +
559H VAL* 3.6 25.3 - - + +
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Residues in contact with HIS 106 (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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67C ARG* 3.4 44.7 + - + +
71C GLU* 2.7 42.5 + - + +
85C ARG* 3.2 7.4 + - - +
96C ILE 3.2 4.9 - - - +
97C SER* 2.9 32.2 + - - -
104C VAL* 3.8 13.6 + - + -
105C GLN* 1.3 76.3 - - - +
107C PHE* 1.3 63.7 + - - +
557H ASP 4.4 1.8 - - - +
558H PTR 3.2 24.6 - - + -
559H VAL* 2.9 28.6 + - - +
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Residues in contact with PHE 107 (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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95C SER* 3.3 6.4 - - - -
96C ILE* 2.7 52.7 + - + +
98C VAL* 3.9 24.7 - - + -
100C HIS* 4.1 21.1 - + - -
105C GLN 4.2 2.5 - - - -
106C HIS* 1.3 74.5 - - - +
108C LYS* 1.3 61.8 + - - +
119C LEU* 4.3 13.5 - - + -
120C TRP* 4.0 6.3 - + - -
139C ILE* 3.3 48.2 - - + -
140C SER* 4.7 1.8 - - - -
558H PTR 3.7 3.6 - - - -
559H VAL* 3.5 41.7 - - + -
560H ASN* 3.4 17.5 - - + +
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Residues in contact with LYS 108 (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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87C SER* 4.1 7.5 + - - -
89C SER* 5.2 0.2 + - - -
90C SER* 3.9 12.8 + - - -
93C ASP* 2.9 36.2 + - - +
94C PHE 4.0 4.7 - - - +
95C SER* 5.1 1.0 + - - -
107C PHE* 1.3 73.2 - - - +
109C VAL* 1.3 74.1 + - - +
110C MET* 3.3 17.9 + - - +
119C LEU* 3.4 4.8 - - - +
558H PTR 3.7 35.0 + - + -
560H ASN* 2.8 30.6 + - - +
561H VAL* 3.7 32.8 - - + -
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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