Contacts of the helix formed by residues 102 - 115 (chain H) in PDB entry 1R4N
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 102 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81H ASP 4.1 5.6 - - - +
82H THR* 4.4 1.8 - - - -
100H GLY 4.6 0.7 - - - +
101H ARG* 1.3 89.7 - - + +
103H LYS* 1.3 66.9 + - - +
104H ALA 3.2 1.1 - - - +
105H GLU* 2.9 49.0 + - + +
106H VAL* 2.9 15.9 + - - +
124H PHE* 3.3 44.2 - - + -
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Residues in contact with LYS 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ATP 3.1 59.7 + - - +
56H ALA* 3.3 13.9 + - - +
79H ASP* 4.1 8.3 - - - +
81H ASP* 3.1 25.0 + - + +
82H THR 4.2 5.4 - - - -
83H ILE* 3.5 20.9 - - - +
87H ASN* 3.2 27.0 + - - +
91H GLN* 3.6 12.9 + - - -
94H PHE* 3.5 24.7 - - + -
101H ARG 3.3 3.0 + - - -
102H PRO* 1.3 71.1 - - - +
104H ALA* 1.3 65.3 + - - +
107H ALA* 2.8 27.3 + - - +
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Residues in contact with ALA 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H ALA* 4.6 3.6 - - - -
77H VAL* 4.1 10.2 - - + +
79H ASP* 3.9 32.6 + - + +
102H PRO* 3.2 1.1 - - + +
103H LYS* 1.3 79.4 - - - +
105H GLU* 1.3 63.9 + - - +
107H ALA* 3.4 5.9 - - - +
108H ALA* 3.1 18.0 + - - +
122H PRO* 3.2 11.6 - - + +
123H HIS 3.9 29.8 - - - +
124H PHE* 4.3 4.5 - - + +
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Residues in contact with GLU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F PRO* 4.6 19.2 - - - +
101H ARG* 3.3 24.1 + - - +
102H PRO* 2.9 42.6 + - + +
104H ALA* 1.3 74.8 - - - +
106H VAL* 1.3 55.7 + - - +
108H ALA* 3.1 5.5 + - - +
109H GLU* 2.8 35.1 + - + +
122H PRO* 3.9 16.4 - - + +
124H PHE* 5.7 1.4 - - + +
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Residues in contact with VAL 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ILE* 3.5 22.7 - - + -
93H LEU 3.6 16.2 - - - +
94H PHE* 3.9 5.6 - - + -
98H ASP* 3.5 27.8 - - + +
101H ARG* 3.6 34.3 - - + +
102H PRO 2.9 15.6 + - - +
103H LYS 3.9 0.7 - - - +
105H GLU* 1.3 70.0 - - + +
107H ALA* 1.3 69.8 + - - +
109H GLU* 2.9 16.8 + - - +
110H PHE* 2.8 26.8 + - + +
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Residues in contact with ALA 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H ALA* 4.4 10.5 - - + -
61H CYS* 5.7 0.2 - - - -
64H LEU* 4.0 21.5 - - + -
77H VAL* 4.9 1.6 - - + -
93H LEU* 4.0 14.4 - - + +
94H PHE* 3.8 14.5 - - + -
103H LYS 2.8 24.4 + - - +
104H ALA* 3.4 8.3 - - - +
106H VAL* 1.3 76.1 - - - +
108H ALA* 1.3 62.3 + - - +
110H PHE* 3.8 1.9 - - - +
111H LEU* 3.0 23.0 + - - +
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Residues in contact with ALA 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H LEU* 5.4 0.2 - - - -
77H VAL* 5.4 0.4 - - + +
104H ALA 3.1 5.5 + - - +
105H GLU 3.1 8.5 + - - +
107H ALA* 1.3 76.3 - - - +
109H GLU* 1.3 68.4 + - - +
111H LEU* 4.7 1.1 - - - -
112H ASN* 2.8 39.5 + - - +
120H VAL* 3.4 31.6 - - + +
122H PRO* 3.6 25.4 - - + -
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Residues in contact with GLU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H ASP* 4.3 2.1 - - - +
101H ARG* 2.9 42.3 + - - +
105H GLU* 2.8 18.4 + - + +
106H VAL* 2.9 19.2 + - - +
108H ALA* 1.3 75.6 - - - +
110H PHE* 1.3 67.1 + - - +
112H ASN* 3.6 4.5 + - - +
113H ASP* 3.5 16.3 + - - +
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Residues in contact with PHE 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G PHE* 3.6 19.7 - + - -
96G LEU* 6.2 0.4 - - + -
92H PHE* 3.8 18.8 - + - -
93H LEU* 3.4 35.2 - - + +
95H ARG* 4.1 17.9 - - + -
98H ASP* 6.0 0.7 - - - -
106H VAL* 2.8 20.8 + - + +
107H ALA 3.8 2.7 - - - +
109H GLU* 1.3 75.5 - - + +
111H LEU* 1.3 61.1 + - - +
113H ASP* 2.8 24.3 + - + +
114H ARG* 2.9 67.6 + - + -
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Residues in contact with LEU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G PHE* 4.2 12.1 - - + -
64H LEU* 3.1 53.8 - - + +
65H LYS* 3.6 5.8 - - + +
68H ALA* 3.6 15.5 - - + -
93H LEU* 4.5 8.7 - - + +
107H ALA 3.0 16.9 + - - +
108H ALA* 4.0 1.8 - - - +
110H PHE* 1.3 82.3 - - - +
112H ASN* 1.3 58.2 + - - +
113H ASP 2.9 5.0 + - - -
114H ARG* 4.5 1.3 - - - +
115H VAL* 3.1 41.6 + - + +
118H CYS* 4.1 10.9 - - - +
120H VAL* 4.6 9.4 - - + -
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Residues in contact with ASN 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H ALA* 2.8 34.2 + - - +
109H GLU* 4.0 4.7 - - - +
111H LEU* 1.3 70.7 - - - +
113H ASP* 1.3 58.2 + - - +
115H VAL 4.1 2.4 - - - +
116H PRO 4.0 15.2 - - - +
118H CYS* 3.1 25.8 - - - +
119H ASN* 3.1 2.0 - - - -
120H VAL* 2.5 56.9 + - - +
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Residues in contact with ASP 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G GLN* 3.8 15.9 - - - +
109H GLU* 3.5 10.0 + - + +
110H PHE* 2.8 13.8 + - + +
112H ASN* 1.3 81.2 - - - +
114H ARG* 1.3 67.8 + - - +
115H VAL 3.2 1.5 + - - -
116H PRO* 4.1 8.1 - - - +
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Residues in contact with ARG 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G PHE* 3.1 51.7 + - + +
75G PHE* 4.6 8.8 - - - +
76G LEU 5.4 2.2 - - - +
77G GLN* 3.8 35.2 + - - +
92G PHE* 3.6 44.6 + - - +
95G GLU* 5.1 12.1 + - - +
96G LEU* 5.9 0.2 - - - +
95H ARG* 5.1 6.9 - - - +
110H PHE* 2.9 59.1 + - + +
111H LEU 4.3 0.9 - - - +
113H ASP* 1.3 78.9 + - - +
115H VAL* 1.3 59.5 + - + +
116H PRO* 3.3 10.2 - - - +
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Residues in contact with VAL 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G PHE* 4.0 17.7 - - + -
16H ARG* 3.6 18.2 - - - +
17H TRP* 5.4 0.9 - - + -
68H ALA* 4.1 15.7 - - + +
69H LEU* 4.0 29.2 - - + -
111H LEU* 3.1 33.3 + - + +
112H ASN 4.1 1.9 - - - +
113H ASP 4.1 2.7 - - - -
114H ARG* 1.3 81.6 - - + +
116H PRO* 1.3 68.7 - - + +
118H CYS* 3.0 28.5 + - + +
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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