Contacts of the helix formed by residues 109 - 124 (chain B) in PDB entry 1N2F
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 GLU 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B GLY 3.9 0.6 + - - -
108B MET* 1.3 72.5 - - - +
110B ARG* 1.3 69.8 + - + +
111B GLU* 3.0 32.8 - - + +
112B ALA* 2.8 29.6 + - + +
113B ALA* 2.9 11.7 + - - +
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B MET 3.4 4.8 + - - -
109B GLU* 1.3 71.6 - - - +
111B GLU* 1.3 62.8 + - - +
113B ALA* 3.3 4.4 + - - +
114B GLU* 3.0 54.2 + - + +
140B VAL* 6.3 0.9 - - + -
142B VAL* 3.9 16.4 + - - +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLU* 3.0 25.8 - - + +
110B ARG* 1.3 80.7 - - - +
112B ALA* 1.3 64.1 + - - +
114B GLU* 3.4 13.2 + - - +
115B ALA* 3.2 22.0 + - + +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 4.9 1.4 + - - -
74B GLN* 4.4 11.3 + - - +
108B MET* 3.6 17.9 - - + +
109B GLU* 2.8 30.7 + - + +
111B GLU* 1.3 77.1 - - - +
113B ALA* 1.3 62.4 + - - +
115B ALA* 3.3 7.2 + - - +
116B LEU* 3.0 24.1 + - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 3.7 22.6 - - + +
108B MET* 3.6 21.4 - - + +
109B GLU 2.9 11.2 + - - +
110B ARG* 3.7 11.7 - - - +
112B ALA* 1.3 76.7 - - - +
114B GLU* 1.3 57.3 + - - +
116B LEU* 3.3 2.9 + - - +
117B VAL* 3.0 35.5 + - - +
140B VAL* 3.9 13.9 - - + -
142B VAL* 4.6 4.0 - - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ARG* 3.0 42.4 + - + +
111B GLU* 3.9 12.9 - - - +
113B ALA* 1.3 75.5 - - - +
115B ALA* 1.3 58.2 + - - +
117B VAL* 3.8 6.9 - - - +
118B ALA* 3.0 29.0 + - - +
140B VAL* 4.6 22.4 - - + +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 3.7 17.1 + - - +
111B GLU* 3.2 13.6 + - + +
112B ALA* 3.6 11.2 - - - +
113B ALA 3.2 0.6 - - - -
114B GLU* 1.3 75.6 - - - +
116B LEU* 1.3 59.1 + - - +
118B ALA* 3.3 6.7 + - - +
119B ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B MET* 3.4 32.3 - - + +
68B VAL* 3.8 11.4 - - + -
69B ALA* 3.8 20.0 - - + +
72B ARG* 3.7 8.9 - - - +
74B GLN* 4.6 11.4 - - + +
76B LEU* 3.5 30.1 - - + -
105B LEU* 4.4 9.2 - - + -
108B MET* 4.2 21.8 - - + -
112B ALA 3.0 16.4 + - - +
113B ALA 3.6 4.3 - - - +
115B ALA* 1.3 77.6 - - - +
117B VAL* 1.3 57.9 - - - +
119B ALA* 3.3 1.9 + - - +
120B ALA* 2.8 31.9 + - - +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PHE* 3.6 4.6 - - + -
65B MET* 4.1 9.2 - - - -
103B ILE* 3.5 43.1 - - + -
105B LEU* 4.2 4.9 - - + -
113B ALA 3.0 20.2 + - - +
114B GLU 3.8 4.0 - - - +
116B LEU* 1.3 72.7 - - - +
118B ALA* 1.3 60.2 + - - +
120B ALA* 4.4 4.9 - - - -
121B HIS* 3.0 28.6 + - - +
138B LEU* 3.6 25.4 - - + -
140B VAL* 3.8 23.1 - - + -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU 3.0 19.4 + - - +
115B ALA* 3.6 7.4 - - - +
116B LEU 3.3 0.2 - - - -
117B VAL* 1.3 80.1 - - - +
119B ALA* 1.3 61.4 + - - +
121B HIS* 3.5 15.1 - - - +
122B GLN* 3.6 14.7 + - - +
138B LEU* 5.4 2.0 - - - -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 3.7 20.6 - - + -
72B ARG* 3.1 31.2 - - - +
115B ALA 2.9 9.0 + - - +
116B LEU 3.8 0.4 - - - +
118B ALA* 1.3 74.1 - - - +
120B ALA* 1.3 60.8 + - - +
121B HIS 3.1 1.3 - - - -
122B GLN* 2.9 27.8 + - - +
123B VAL* 3.4 10.4 + - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PHE* 4.0 10.1 - - + -
64B ALA* 3.5 13.2 - - + +
65B MET* 3.7 41.7 - - + +
68B VAL* 3.7 10.2 - - + +
116B LEU 2.8 21.5 + - - +
117B VAL 4.0 0.2 - - - +
119B ALA* 1.3 73.9 - - - +
121B HIS* 1.3 56.1 + - - +
123B VAL* 3.1 1.6 + - - -
124B CYS* 2.9 29.1 + - - +
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Residues in contact with HIS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TYR* 4.4 0.7 - - - -
61B PHE* 3.8 11.2 - + + -
117B VAL 3.0 18.3 + - - +
118B ALA* 3.5 9.8 + - - +
119B ALA 3.1 0.2 - - - -
120B ALA* 1.3 78.1 - - - +
122B GLN* 1.3 64.5 + - - +
127B SER* 2.9 43.2 + - - -
131B ARG* 2.9 42.3 + - - -
136B VAL* 4.2 24.6 - - + +
138B LEU* 3.5 28.8 - - + +
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE* 5.3 0.2 - - - +
92A PRO 5.5 0.5 - - - +
93A GLY 3.6 10.3 - - - +
118B ALA 3.6 14.3 + - - +
119B ALA* 2.9 11.5 + - - +
121B HIS* 1.3 83.9 + - - +
123B VAL* 1.3 62.6 + - + +
128B ASN* 3.1 22.5 + - - +
131B ARG* 3.6 33.3 + - - +
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLY 3.2 21.8 - - - +
94A GLY* 3.6 12.8 - - - -
95A PHE* 3.0 35.4 + - + -
64B ALA* 4.4 4.3 - - + -
67B PHE* 3.8 27.8 - - + -
68B VAL* 4.1 15.0 - - + -
71B GLN* 5.8 1.6 - - - +
119B ALA 3.7 11.2 - - - +
120B ALA* 3.1 9.7 + - - +
122B GLN* 1.3 81.0 - - + +
124B CYS* 1.3 64.5 + - - +
125B PRO* 3.2 2.8 - - - +
128B ASN* 3.5 2.0 + - - -
172B DTT 4.3 9.4 - - - -
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Residues in contact with CYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TYR* 3.7 27.1 - - - -
60B CYS* 3.7 22.4 - - - -
61B PHE* 4.1 15.0 - - + -
64B ALA* 4.0 6.0 - - + +
120B ALA 2.9 15.4 + - - +
121B HIS 4.2 0.4 + - - +
122B GLN 3.7 0.2 - - - -
123B VAL* 1.3 74.7 - - - +
125B PRO* 1.3 68.7 - - - +
126B TYR* 3.7 10.5 - - - -
127B SER* 3.0 15.4 + - - +
128B ASN* 2.9 28.6 + - - -
172B DTT 4.0 5.2 - - - -
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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