Contacts of the helix formed by residues 145 - 152 (chain U) in PDB entry 3IS7
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 GLY 145 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C GLU* 3.9 14.2 + - - -
141U ILE 2.9 17.7 + - - -
142U GLN 4.2 1.3 + - - -
143U LYS 3.6 1.6 - - - -
144U VAL* 1.3 79.7 - - - +
146U LEU* 1.3 61.4 + - - -
147U GLU 3.4 2.2 - - - -
148U ASN 3.4 1.0 + - - -
149U TYR* 2.8 30.3 + - - +
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Residues in contact with LEU 146 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143S LYS 5.3 2.5 - - - +
83U THR* 5.4 0.4 - - - -
84U GLN* 3.5 40.4 - - - +
141U ILE* 3.6 33.0 + - + +
145U GLY* 1.3 73.1 - - - -
147U GLU* 1.3 62.7 + - + +
149U TYR* 3.3 2.1 + - + -
150U LEU* 2.9 55.4 + - + +
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Residues in contact with GLU 147 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142S GLN 4.3 3.5 - - - +
143S LYS 3.9 18.1 - - - +
144S VAL* 3.2 19.9 - - - +
145S GLY* 3.1 28.4 + - - -
148S ASN* 3.7 8.4 + - - +
145U GLY 3.4 0.6 - - - -
146U LEU* 1.3 79.9 - - + +
148U ASN* 1.3 58.2 + - - +
150U LEU* 3.3 2.6 + - - +
151U GLN* 2.9 29.5 + - - +
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Residues in contact with ASN 148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C GLU* 3.7 17.2 + - - +
148C ASN* 3.0 23.7 + - - +
151C GLN* 2.8 38.9 + - + +
160C K 3.0 10.6 - - - -
148S ASN* 3.0 21.9 + - - +
144U VAL* 3.1 32.8 + - + +
145U GLY 3.4 1.4 + - - -
146U LEU 3.3 0.2 - - - -
147U GLU* 1.3 76.9 - - - +
149U TYR* 1.3 62.4 + - - +
151U GLN* 3.3 0.9 + - - -
152U SER* 3.0 11.8 + - - -
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Residues in contact with TYR 149 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C MET* 4.4 5.8 - - + -
40U LEU* 3.7 21.6 - - + +
83U THR* 4.3 15.5 - - + -
87U LEU* 4.2 2.1 - - + +
137U GLN* 2.8 56.8 + - + +
140U LEU* 3.8 22.7 - - + -
141U ILE* 3.6 32.8 - - + -
144U VAL* 3.6 9.8 - - + +
145U GLY 2.8 21.6 + - - +
146U LEU* 3.8 3.4 - - + +
148U ASN* 1.3 73.6 - - - +
150U LEU* 1.3 70.2 + - + +
152U SER* 3.4 5.5 + - - -
153U HIS* 2.9 48.7 + + - -
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Residues in contact with LEU 150 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143S LYS* 3.7 36.6 - - + +
144S VAL* 3.9 12.6 - - + -
37U LEU* 3.3 31.9 - - + +
40U LEU* 4.6 2.7 - - + -
83U THR* 3.3 42.0 - - + +
84U GLN* 5.4 1.1 - - - +
146U LEU* 2.9 40.7 + - + +
147U GLU 3.9 2.7 - - - +
149U TYR* 1.3 81.3 - - + +
151U GLN* 1.3 65.9 + - - +
153U HIS* 3.0 12.0 + - - -
154U MET* 3.4 4.2 + - - +
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Residues in contact with GLN 151 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C GLN* 2.9 14.3 + - - +
160C K 2.9 21.3 - - - -
144S VAL* 3.8 13.4 - - + +
148S ASN* 2.8 31.1 + - + +
151S GLN* 2.8 27.0 + - - +
152S SER* 2.7 31.4 + - - +
147U GLU 2.9 18.1 + - - +
148U ASN 3.3 2.9 + - - +
150U LEU* 1.3 77.4 - - - +
152U SER* 1.3 60.8 + - - +
153U HIS 3.1 1.6 + - - -
154U MET* 3.3 24.0 + - - +
155U HIS* 4.7 0.7 + - - -
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Residues in contact with SER 152 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C GLN* 2.9 37.0 + - - +
154C MET* 3.9 23.4 - - - -
155C HIS* 3.2 26.8 - - - -
39U ARG* 3.6 8.0 + - - -
148U ASN 3.0 8.4 + - - -
149U TYR 3.8 6.1 - - - -
150U LEU 3.3 0.6 - - - -
151U GLN* 1.3 75.2 - - - +
153U HIS* 1.3 59.1 + - - +
154U MET 3.6 0.4 - - - -
155U HIS 4.6 3.1 - - - +
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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