Contacts of the helix formed by residues 98 - 107 (chain D) in PDB entry 5IRC
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 LYS 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1289B LYS* 3.9 25.1 - - + +
13D ASP* 5.3 0.7 - - - +
62D GLY 4.8 1.2 + - - -
64D GLU* 4.2 14.3 - - - +
67D ASP* 2.8 38.0 + - - +
70D ARG* 4.2 1.0 - - - +
94D ASN* 2.8 19.8 + - + +
96D PRO 3.4 0.2 - - - -
97D GLU* 1.3 82.0 - - + +
99D TRP* 1.3 104.1 + - + +
100D THR 3.4 1.6 - - - -
101D PRO* 3.3 5.7 - - - +
102D GLU* 3.3 37.7 + - + +
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Residues in contact with TRP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 4.1 14.1 - - + -
12D GLY* 3.3 39.9 - - - -
13D ASP* 2.8 30.9 + - - +
62D GLY* 3.6 21.1 - - - -
70D ARG* 3.6 50.3 - - - -
74D TYR* 5.0 1.1 - - - -
82D MET* 3.8 25.4 - - + -
83D CYS 4.9 0.4 - - - -
91D SER 5.0 1.1 - - - -
94D ASN* 3.0 27.2 + - + -
95D ILE* 3.9 11.9 - - + +
98D LYS* 1.3 96.4 - - + +
100D THR* 1.3 61.4 + - - +
102D GLU* 3.4 8.2 + - - +
103D VAL* 2.9 34.7 + - - +
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Residues in contact with THR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242A TRP* 3.5 40.4 - - + -
82D MET* 3.7 19.7 - - + +
95D ILE 2.8 24.2 + - - -
96D PRO* 4.1 4.3 - - - -
99D TRP* 1.3 75.9 - - - +
101D PRO* 1.4 66.6 - - - +
103D VAL* 3.2 0.9 + - - -
104D LYS* 2.9 36.6 + - + +
112D ILE* 5.8 0.7 - - + -
151D ILE* 3.4 25.3 - - + +
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Residues in contact with PRO 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A GLY* 6.0 1.3 - - - -
1242A TRP* 3.8 27.1 - - + +
96D PRO 3.2 22.4 - - - +
97D GLU 3.7 17.0 - - - +
98D LYS* 3.3 15.7 - - - +
100D THR* 1.4 90.0 - - - +
102D GLU* 1.3 59.7 + - - +
104D LYS* 4.0 1.8 - - + +
105D HIS* 3.1 24.8 + - - +
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Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ASP* 4.2 9.4 - - - +
70D ARG* 3.0 39.1 + - - +
71D PRO* 5.6 0.2 - - - -
74D TYR* 2.7 30.2 + - - +
98D LYS* 3.3 27.5 + - + +
99D TRP* 3.7 10.7 - - - +
100D THR 3.2 0.6 - - - -
101D PRO* 1.3 78.3 - - - +
103D VAL* 1.3 64.5 + - + +
105D HIS* 3.3 4.8 + - - +
106D PHE* 3.2 48.7 + - + -
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 4.0 15.9 - - + -
74D TYR* 4.0 19.5 - - - +
80D ILE* 3.5 33.2 - - + -
82D MET* 3.8 15.0 - - + -
99D TRP* 2.9 20.7 + - + +
100D THR 4.0 0.7 - - - +
102D GLU* 1.3 76.3 - - + +
104D LYS* 1.3 57.4 + - + +
106D PHE* 5.2 0.7 - - - -
107D CYS* 2.7 40.6 + - - +
110D VAL 5.6 0.2 - - - +
112D ILE* 3.7 27.1 - - + -
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Residues in contact with LYS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242A TRP* 4.0 26.0 - - + -
100D THR* 2.9 33.5 + - + +
101D PRO 4.1 1.8 - - - +
103D VAL* 1.3 77.5 - - - +
105D HIS* 1.3 61.3 + - - +
107D CYS 5.1 1.3 - - - +
108D PRO* 3.3 47.3 + - + +
110D VAL 4.9 4.9 + - - -
112D ILE* 4.1 24.3 - - + +
151D ILE 3.8 22.1 + - - -
152D GLY* 4.9 6.3 + - - -
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Residues in contact with HIS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PRO 3.1 18.1 + - - +
102D GLU* 3.6 5.6 - - - +
103D VAL 3.1 1.0 - - - -
104D LYS* 1.3 80.0 - - - +
106D PHE* 1.3 93.7 + + - +
108D PRO* 4.1 5.5 - - - +
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Residues in contact with PHE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D PRO* 3.6 35.7 - - + -
74D TYR* 3.5 38.8 - + + +
102D GLU* 3.2 36.7 + - + +
103D VAL 4.4 0.4 - - - +
105D HIS* 1.3 104.8 - + - +
107D CYS* 1.3 65.7 + - - +
108D PRO* 3.6 5.4 - - - +
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Residues in contact with CYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D TYR* 3.7 47.6 - - - -
77D THR* 4.5 3.4 - - - -
80D ILE* 4.3 13.7 - - + -
103D VAL* 2.7 24.4 + - - +
104D LYS* 4.6 1.9 - - - +
106D PHE* 1.3 82.2 - - - +
108D PRO* 1.3 67.0 - - - +
109D ASN 3.0 4.5 + - - -
110D VAL* 3.2 37.9 + - + +
112D ILE* 6.0 0.2 - - - +
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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