Contacts of the helix formed by residues 101 - 119 (chain B) in PDB entry 2PEG
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 ASP 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B TRP* 5.2 2.6 + - - -
99B ASP* 2.9 17.1 + - - +
100B PRO* 1.3 80.2 - - - +
102B ASN* 1.3 64.0 + - - +
103B PHE 3.2 1.3 + - - -
104B LYS* 3.3 18.6 + - - +
105B LEU* 3.4 32.3 + - - +
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Residues in contact with ASN 102 (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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31B CYS* 5.0 1.4 - - - -
37B TRP* 4.2 9.7 + - - -
38B THR* 3.8 21.6 - - + +
40B ARG* 4.8 5.7 + - - +
41B HIS* 3.9 10.5 + - - -
98B VAL* 3.6 19.0 - - + +
99B ASP* 3.0 30.1 + - - +
101B ASP* 1.3 80.7 - - - +
103B PHE* 1.3 57.6 + - - +
105B LEU* 3.3 15.0 + - - +
106B LEU* 3.0 29.5 + - - +
400B HEM 3.8 27.8 - - + +
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Residues in contact with PHE 103 (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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92B HIS* 3.8 29.8 - + + -
98B VAL* 3.8 13.9 - - + -
99B ASP 4.1 3.8 - - - -
100B PRO* 3.4 33.0 - - + +
101B ASP 3.2 1.2 - - - -
102B ASN* 1.3 76.3 - - - +
104B LYS* 1.3 57.3 + - - +
106B LEU* 3.8 2.6 - - - +
107B SER* 2.9 28.9 + - - +
138B VAL* 3.5 26.3 - - + +
141B LEU* 3.8 41.1 - - + -
142B GLY* 3.9 13.2 - - - -
400B HEM 3.5 46.9 - + + +
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Residues in contact with LYS 104 (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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100B PRO 4.5 1.0 + - - +
101B ASP* 3.3 17.0 + - - +
103B PHE* 1.3 74.7 - - - +
105B LEU* 1.3 71.2 + - + +
107B SER* 3.2 11.5 + - - +
108B ASP* 3.0 52.5 + - - +
138B VAL* 4.0 16.9 - - + +
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Residues in contact with LEU 105 (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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31B CYS* 4.4 5.4 - - - -
35B TYR* 3.6 49.8 - - + +
37B TRP* 3.7 30.1 - - + +
38B THR* 4.8 2.2 - - + -
101B ASP* 3.4 33.4 - - - +
102B ASN* 3.3 15.4 + - - +
104B LYS* 1.3 83.0 - - + +
106B LEU* 1.3 61.4 + - - +
108B ASP* 3.3 8.1 + - - +
109B CYS* 3.2 23.7 + - - -
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Residues in contact with LEU 106 (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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27B ALA* 3.9 16.6 - - + +
28B LEU* 4.1 17.0 - - + +
31B CYS* 3.8 30.2 - - + -
67B VAL* 4.3 17.9 - - + -
102B ASN 3.0 17.8 + - - +
103B PHE 3.8 3.4 - - - +
105B LEU* 1.3 77.6 - - - +
107B SER* 1.3 57.8 + - - +
109B CYS* 3.0 2.6 + - - +
110B ILE* 2.9 39.4 + - + +
400B HEM 3.7 51.8 - - + -
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Residues in contact with SER 107 (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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103B PHE 2.9 17.8 + - - +
104B LYS* 3.2 13.3 + - - +
106B LEU* 1.3 78.9 - - - +
108B ASP* 1.3 62.9 + - - +
110B ILE* 3.8 12.1 - - - -
111B THR* 4.2 10.4 - - - -
134B LEU* 3.3 35.5 - - - +
135B ALA* 5.0 0.3 - - - -
138B VAL* 3.8 17.9 - - - +
400B HEM 6.6 0.4 - - - +
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Residues in contact with ASP 108 (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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104A HIS* 3.7 32.2 + - + +
35B TYR* 4.7 13.3 + - + +
104B LYS* 3.0 44.5 + - - +
105B LEU* 3.6 11.6 - - - +
106B LEU 3.3 0.2 - - - -
107B SER* 1.3 74.7 - - - +
109B CYS* 1.3 59.5 + - - +
110B ILE 3.4 0.2 - - - -
111B THR* 3.5 6.4 + - - -
112B ILE* 3.0 38.8 + - + +
131B GLN* 5.7 1.7 - - - +
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Residues in contact with CYS 109 (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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123A HIS* 4.7 8.5 - - - -
27B ALA* 3.5 21.3 - - - +
30B ARG* 4.1 15.7 - - + +
31B CYS* 3.5 31.0 - - + +
34B VAL* 4.7 0.7 - - - -
35B TYR* 3.9 16.2 - - - -
105B LEU 3.2 13.6 + - - -
106B LEU 3.0 9.4 + - - +
108B ASP* 1.3 77.7 - - - +
110B ILE* 1.3 59.6 + - - +
112B ILE* 3.3 6.1 + - - +
113B VAL* 2.9 34.1 + - - +
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Residues in contact with ILE 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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18B MET* 5.6 2.5 - - + -
23B ILE* 5.0 7.7 - - + +
27B ALA* 3.8 24.0 - - + +
67B VAL* 4.1 17.9 - - + -
68B LEU* 4.5 14.4 - - + -
71B LEU* 4.1 24.0 - - + -
106B LEU* 2.9 30.1 + - + +
107B SER* 4.4 7.6 - - - -
109B CYS* 1.3 76.0 - - - +
111B THR* 1.3 62.7 + - - +
113B VAL* 3.3 1.9 + - - +
114B LEU* 2.9 24.4 + - + +
130B PHE* 3.7 24.5 - - + -
134B LEU* 4.3 12.1 - - + -
400B HEM 5.1 4.0 - - + -
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Residues in contact with THR 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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104A HIS* 4.3 2.7 - - - +
108A VAL* 4.2 12.6 - - + -
107B SER* 4.2 4.5 - - - -
108B ASP* 3.5 13.8 + - - -
109B CYS 3.3 0.2 - - - -
110B ILE* 1.3 78.5 - - - +
112B ILE* 1.3 59.4 + - - +
114B LEU* 3.4 2.3 + - - +
115B ALA* 2.9 28.1 + - - +
122B PHE* 3.9 24.5 - - + -
130B PHE* 3.6 23.6 - - - -
131B GLN* 3.7 32.1 - - + +
134B LEU* 3.7 10.4 - - - +
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Residues in contact with ILE 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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104A HIS* 4.3 13.2 - - + +
107A LEU* 4.0 21.3 - - + -
108A VAL* 4.3 22.2 - - + +
111A SER* 2.8 36.2 + - - +
118A PHE* 3.9 20.2 - - + -
123A HIS* 3.5 35.2 - - + +
30B ARG* 4.1 9.9 - - - +
108B ASP* 3.0 25.7 + - + +
109B CYS 3.9 3.6 - - - +
111B THR* 1.3 77.7 - - - +
113B VAL* 1.3 63.3 + - - +
115B ALA* 3.4 5.9 + - - +
116B ALA 3.1 7.4 + - - -
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Residues in contact with VAL 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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23B ILE* 3.8 29.4 - - + +
26B LYS* 3.8 30.1 - - + -
27B ALA* 3.8 23.1 - - + +
30B ARG* 3.7 26.5 - - - +
109B CYS 2.9 20.8 + - - +
110B ILE 3.9 2.9 - - - +
112B ILE* 1.3 73.5 - - - +
114B LEU* 1.3 66.6 + - - +
116B ALA* 3.1 10.3 + - + +
117B LYS* 3.0 19.2 + - - +
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Residues in contact with LEU 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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14B ILE* 3.7 15.5 - - + +
18B MET* 2.8 39.7 - - + -
23B ILE* 4.7 4.2 - - + +
110B ILE* 2.9 17.7 + - + +
111B THR 3.6 5.2 - - - +
113B VAL* 1.3 79.8 - - - +
115B ALA* 1.3 51.5 + - - +
117B LYS* 3.1 20.0 + - + -
118B MET* 2.8 54.8 + - - +
122B PHE* 3.7 20.4 - - + -
130B PHE* 3.6 23.8 - - + -
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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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108A VAL* 3.9 14.8 - - + +
111A SER* 4.3 1.3 - - - -
112A THR* 3.5 26.6 - - + +
111B THR 2.9 18.1 + - - +
112B ILE* 3.5 9.6 - - - +
114B LEU* 1.3 75.4 - - - +
116B ALA* 1.3 53.8 + - - +
119B GLY* 2.7 33.1 + - - -
122B PHE* 3.7 26.4 - - + -
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Residues in contact with ALA 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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111A SER* 3.3 33.3 + - - +
112A THR 5.1 0.3 - - - +
115A PRO* 3.9 30.2 - - + +
30B ARG* 6.0 4.0 - - - +
112B ILE 3.1 7.3 + - - +
113B VAL* 3.1 12.5 + - + +
115B ALA* 1.3 77.3 - - - +
117B LYS* 1.3 59.7 + - - +
119B GLY* 3.8 5.5 + - - -
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Residues in contact with LYS 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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14B ILE 5.6 1.1 - - - -
17B HIS* 3.5 35.3 + - - +
18B MET* 4.3 7.6 - - - +
19B ASP 5.2 2.0 - - - +
22B ASP* 5.7 2.5 - - - +
23B ILE* 4.0 21.3 - - + -
113B VAL 3.0 12.1 + - - +
114B LEU* 3.6 17.3 - - + +
116B ALA* 1.3 79.4 - - - +
118B MET* 1.3 91.4 + - + +
119B GLY* 3.5 0.5 + - - -
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Residues in contact with MET 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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14B ILE* 4.5 17.3 - - + -
114B LEU* 2.8 42.4 + - - +
117B LYS* 1.3 101.4 - - + +
119B GLY* 1.3 63.3 + - - +
120B HIS 3.3 0.7 + - - -
121B ALA* 3.1 48.7 + - + +
122B PHE* 3.9 19.7 - - + +
126B THR* 4.3 11.9 - - + +
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Residues in contact with GLY 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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112A THR* 3.6 29.7 - - - +
115B ALA 2.7 21.1 + - - -
116B ALA 3.8 3.5 + - - -
117B LYS 3.3 4.0 + - - -
118B MET* 1.3 71.6 - - - +
120B HIS* 1.3 58.2 + - - -
122B PHE* 2.9 25.3 + - - +
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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