Contacts of the helix formed by residues 98 - 114 (chain A) 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 ASN 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 4.7 0.3 - - - +
38A GLN* 3.9 13.9 - - - +
39A THR* 3.5 21.7 - - + +
42A TYR* 3.9 12.2 + - - -
95A ASP* 3.1 32.7 - - - +
96A PRO 3.0 1.2 - - - -
97A ALA* 1.3 82.6 - - - +
99A PHE* 1.3 64.5 + - - +
100A LYS 3.3 1.1 - - - -
101A ILE* 3.1 35.2 + - - +
102A LEU 3.1 10.6 + - - -
200A HEM 3.4 31.6 - - + +
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS* 4.0 14.6 - + + -
94A VAL* 4.5 5.6 - - + -
96A PRO* 3.2 33.8 + - + +
98A ASN* 1.3 77.9 - - - +
100A LYS* 1.3 63.9 + - - +
101A ILE 3.2 0.2 + - - -
102A LEU* 3.3 3.0 + - - +
103A ASN* 3.0 29.3 + - - +
134A ALA* 3.8 31.4 - - + -
137A LEU* 3.8 33.7 - - + -
138A ALA* 4.3 1.8 - - + -
141A TYR* 3.4 40.6 - + - -
200A HEM 3.7 42.5 - + + +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PRO 4.7 0.6 + - - +
97A ALA* 2.8 43.5 + - - +
99A PHE* 1.3 80.0 - - - +
101A ILE* 1.3 67.5 + - + +
103A ASN* 3.5 12.7 - - - +
104A HIS* 3.0 27.4 + - - +
134A ALA* 4.7 5.5 - - + +
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Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 3.9 13.2 - - + -
36A TYR* 3.3 51.8 - - + -
38A GLN* 3.7 19.7 - - - +
39A THR* 4.7 0.9 - - + -
97A ALA* 4.0 12.3 - - + +
98A ASN* 3.1 34.4 + - + +
100A LYS* 1.3 83.4 - - + +
102A LEU* 1.3 65.6 + - - +
104A HIS* 3.2 7.1 + - - +
105A CYS* 3.0 22.0 + - - -
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 4.1 32.3 - - + +
29A LEU* 4.5 6.7 - - + +
32A MET* 3.7 29.8 - - + -
63A VAL* 4.0 21.8 - - + -
98A ASN 3.1 9.8 + - - +
99A PHE 3.9 6.3 - - - +
101A ILE* 1.3 76.4 - - - +
103A ASN* 1.3 58.6 + - - +
105A CYS* 3.0 3.6 + - + -
106A ILE* 2.8 41.9 + - + +
200A HEM 3.5 46.7 - - + -
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 3.0 19.9 + - - +
100A LYS* 3.5 13.2 - - - +
101A ILE 3.2 0.2 - - - -
102A LEU* 1.3 76.9 - - - +
104A HIS* 1.3 62.6 + - - +
106A ILE* 3.1 7.4 + - - +
107A LEU* 3.0 27.8 + - + +
127A ASP* 6.1 0.9 - - - +
130A LEU* 3.0 61.9 + - + +
131A SER* 4.4 1.0 - - - +
133A VAL* 5.1 1.2 - - - +
134A ALA* 3.7 15.4 - - - +
200A HEM 3.7 17.8 - - - +
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Residues in contact with HIS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.3 24.2 - + - +
100A LYS 3.0 14.4 + - - +
101A ILE* 3.2 9.6 + - - +
103A ASN* 1.3 75.8 - - - +
105A CYS* 1.3 64.1 + - - +
107A LEU* 3.2 12.4 + - - +
108A VAL* 3.0 37.9 + - + +
108B ASP* 3.7 42.7 + - + +
111B THR* 4.3 3.2 - - + +
112B ILE* 4.3 14.2 - - + +
127B GLN* 4.1 6.3 - - - -
131B GLN* 2.9 24.6 + - - -
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Residues in contact with CYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.7 22.7 - - - +
31A ARG* 4.2 10.3 - - + +
32A MET* 3.8 25.4 - - - -
36A TYR* 3.7 26.9 - - - -
101A ILE 3.0 18.1 + - - +
102A LEU* 3.5 8.7 - - - +
104A HIS* 1.3 79.4 - - - +
106A ILE* 1.3 55.0 + - - +
108A VAL* 3.3 9.0 + - - +
109A VAL* 3.0 33.8 + - - +
127B GLN* 4.4 6.5 - - - +
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Residues in contact with ILE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.4 1.8 - - + -
28A ALA* 3.8 21.3 - - + -
63A VAL* 4.7 3.1 - - + -
64A MET* 4.1 33.2 - - + -
67A ILE* 4.2 9.9 - - + -
102A LEU* 2.8 33.5 + - + +
103A ASN* 3.1 12.3 + - - +
105A CYS* 1.3 73.7 - - - +
107A LEU* 1.3 66.1 + - - +
109A VAL* 3.3 3.7 + - - +
110A ILE* 2.9 44.4 + - + +
126A LEU* 5.5 0.2 - - + -
130A LEU* 4.5 13.2 - - + -
200A HEM 4.2 17.7 - - + -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN* 3.0 18.7 + - + +
104A HIS* 3.2 13.9 + - - +
106A ILE* 1.3 75.9 - - - +
108A VAL* 1.3 62.4 - - - +
110A ILE* 3.4 3.8 + - - +
111A SER* 2.9 25.7 + - - -
118A PHE* 3.9 18.3 - - + -
123A HIS* 4.0 19.7 - - + +
126A LEU* 3.7 26.7 - - + -
127A ASP* 3.9 24.2 - - - +
130A LEU* 3.5 24.9 - - + -
112B ILE* 4.0 18.8 - - + -
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 4.0 28.0 - - - +
104A HIS* 3.0 43.2 + - + +
105A CYS* 3.6 9.4 - - - +
107A LEU* 1.3 76.7 - - - +
109A VAL* 1.3 58.9 + - - +
111A SER* 3.2 8.5 + - - -
112A THR* 2.9 27.7 + - + +
111B THR* 4.2 12.3 - - + -
112B ILE* 4.3 8.3 - - + -
115B ALA* 3.9 3.9 - - + +
122B PHE* 4.1 18.2 - - + -
127B GLN* 3.9 15.5 - - - +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.7 19.7 - - + +
27A ASP* 3.6 26.0 - - + +
28A ALA* 3.5 24.2 - - - +
31A ARG* 3.6 24.0 - - - +
105A CYS 3.0 22.0 + - - +
106A ILE* 3.8 4.3 - - - +
108A VAL* 1.3 73.7 - - - +
110A ILE* 1.3 66.0 + - - +
112A THR* 2.8 22.8 + - - -
113A MET* 2.9 27.0 + - - +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.9 2.7 - - + -
14A TRP* 5.6 1.1 - - + -
17A ILE* 3.7 32.5 - - + -
24A ILE* 4.2 18.2 - - + -
64A MET* 5.2 3.1 - - + -
106A ILE* 2.9 38.6 + - + +
107A LEU* 3.8 4.9 - - - +
109A VAL* 1.3 75.4 - - - +
111A SER* 1.3 56.0 + - - +
113A MET* 4.5 0.7 - - - +
114A PHE* 2.7 47.0 + - + +
118A PHE* 3.7 28.7 - - + -
126A LEU* 3.7 24.0 - - + -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU 2.9 17.9 + - - -
108A VAL 3.4 5.6 - - - -
109A VAL 3.2 0.2 - - - -
110A ILE* 1.3 77.4 - - - +
112A THR* 1.3 60.7 + - - +
113A MET 3.4 0.3 + - - -
115A PRO* 3.5 16.3 - - - +
118A PHE* 3.8 22.2 - - - +
30B ARG* 5.5 1.2 + - - -
112B ILE* 2.8 37.3 + - - +
115B ALA* 4.3 2.7 - - - -
116B ALA* 3.3 26.3 - - - +
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Residues in contact with THR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP* 4.4 4.2 + - - -
31A ARG* 4.4 12.1 + - - +
108A VAL* 2.9 22.3 + - + +
109A VAL* 2.8 20.6 + - - -
111A SER* 1.3 77.1 - - - +
113A MET* 1.3 67.7 + - - +
115A PRO* 4.0 6.4 - - - +
115B ALA* 3.5 32.8 - - + +
116B ALA* 4.6 0.7 - - - +
119B GLY* 3.6 36.6 - - - +
120B HIS* 4.0 13.7 + - - -
122B PHE* 4.3 8.1 - - + -
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Residues in contact with MET 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A SER* 5.2 3.1 - - - -
23A ALA* 3.8 26.2 - - + +
24A ILE* 3.8 20.6 - - - -
27A ASP* 3.0 28.7 - - + +
109A VAL* 2.9 31.2 + - + +
112A THR* 1.3 83.8 - - - +
114A PHE* 1.3 86.3 + - + +
115A PRO* 3.4 7.3 - - - +
120B HIS* 3.6 23.8 - - + +
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS 4.4 1.8 - - - -
17A ILE* 3.5 48.0 - - + -
19A LYS* 4.2 17.5 - - - -
20A SER* 3.6 34.1 - - - -
24A ILE* 4.2 9.2 - - + -
110A ILE* 2.7 29.7 + - + +
111A SER 4.0 0.2 - - - -
113A MET* 1.3 97.4 - - + +
115A PRO* 1.3 59.7 - - - +
116A LYS 3.1 3.0 + - - -
117A GLU* 3.2 28.9 + - + +
118A PHE* 2.8 28.1 + - - +
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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