Contacts of the strand formed by residues 157 - 162 (chain S) in PDB entry 3HOU
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 ILE 157 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S CYS* 3.9 11.2 - - - -
39S THR 4.1 7.4 - - - +
40S GLY* 4.8 1.1 - - - -
43S GLY* 3.7 30.1 - - - -
44S TYR* 3.5 13.8 + - + -
80S LYS* 4.1 15.9 - - + +
81S PRO* 3.9 26.7 - - + -
106S MET* 3.2 21.2 - - - +
107S LYS 4.5 1.2 + - - -
150S CYS* 4.1 23.8 - - + -
151S ILE 4.0 2.7 - - - -
152S SER* 3.9 23.3 - - - +
153S GLN* 6.0 0.4 - - - -
156S SER* 1.3 84.0 - - - +
158S HIS* 1.3 66.2 + - - +
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Residues in contact with HIS 158 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G HIS* 2.9 60.3 + + + +
100S GLU* 3.5 20.0 + - - -
106S MET* 4.6 1.1 - - - -
107S LYS* 3.1 31.0 + - + +
108S VAL 4.3 0.2 - - - -
109S PHE* 4.1 7.7 - - - +
150S CYS* 3.2 3.2 - - - +
151S ILE* 2.5 51.6 + - + +
153S GLN* 5.5 4.0 - - + +
157S ILE* 1.3 76.3 + - - +
159S ALA* 1.3 85.3 + - - +
160S ILE* 5.3 0.2 - - + -
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Residues in contact with ALA 159 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106S MET* 5.1 2.4 - - - -
107S LYS 3.6 4.6 + - - +
108S VAL* 3.5 6.1 - - + -
109S PHE 2.8 22.8 + - - -
147S ILE* 3.4 25.1 - - + -
149S GLY 2.9 15.9 - - - +
150S CYS* 3.3 20.2 - - - -
151S ILE* 5.1 2.0 - - - -
158S HIS* 1.3 83.4 - - - +
160S ILE* 1.3 70.3 + - - +
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Residues in contact with ILE 160 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G THR* 4.1 30.3 - - + +
113G HIS* 5.3 0.4 - - - +
114G LEU* 5.7 0.9 - - + -
160G ILE* 4.6 21.1 - - + -
108S VAL* 4.1 3.1 - - - -
109S PHE* 2.8 34.1 - - + +
111S THR* 4.4 3.8 - - - +
114S LEU* 3.5 24.7 - - + -
147S ILE* 3.6 1.1 - - - -
148S GLU* 2.6 39.2 + - + +
149S GLY 2.9 11.9 + - - +
151S ILE* 5.2 11.0 - - + -
158S HIS* 5.3 1.6 - - + -
159S ALA* 1.3 81.9 - - - +
161S GLY* 1.3 52.1 + - - +
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Residues in contact with GLY 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108S VAL* 3.8 5.7 - - - +
109S PHE 2.8 7.3 + - - -
110S VAL* 2.6 35.3 - - - +
114S LEU* 3.4 8.0 - - - +
145S VAL* 4.0 8.7 - - - -
146S LYS 2.9 17.9 - - - -
147S ILE* 4.1 1.3 - - - -
148S GLU* 3.6 5.4 - - - -
160S ILE* 1.3 75.8 - - - +
162S SER* 1.3 57.1 + - - -
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Residues in contact with SER 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110S VAL* 4.0 0.4 - - - -
114S LEU* 3.3 25.4 - - - -
146S LYS* 3.0 24.2 + - - +
148S GLU* 2.4 35.1 + - - +
161S GLY* 1.3 73.8 - - - -
163S ILE* 1.3 71.2 + - - +
164S LYS* 3.6 6.7 - - - -
165S GLU* 3.3 17.1 + - - +
168S LEU* 3.5 5.5 - - - +
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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