Contacts of the strand formed by residues 121 - 127 (chain T) 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 LEU 121 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537M ARG* 3.6 26.5 - - + +
540M PHE* 3.9 25.6 - - + -
565M ILE* 4.7 2.9 - - + -
23T VAL* 3.8 34.8 - - + -
41T ASP* 3.7 28.0 - - + +
43T ASN 4.2 3.4 - - - +
95T TYR* 4.1 15.5 - - - +
97T MET* 4.3 7.9 - - - -
117T SER* 3.5 0.2 - - - -
118T PHE* 2.6 52.7 + - + +
119T GLY 3.6 1.1 - - - +
120T GLY* 1.3 71.3 - - - +
122T LEU* 1.3 58.3 + - - +
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Residues in contact with LEU 122 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537M ARG* 3.4 21.3 - - - +
598M LEU* 3.4 31.4 - - + +
599M SER 4.2 0.9 - - - +
613M ILE 3.8 8.1 - - - +
614M PHE* 3.9 13.0 - - + -
25T ARG* 4.0 4.0 - - - +
40T LEU* 3.9 2.6 - - - +
41T ASP* 2.9 39.9 + - - +
102T TYR* 3.1 28.3 - - + +
116T TYR 3.2 3.6 - - - +
117T SER* 3.2 31.6 - - - +
120T GLY 3.2 11.0 + - - +
121T LEU* 1.3 73.7 - - - +
123T MET* 1.3 65.7 + - - +
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Residues in contact with MET 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598M LEU* 4.2 5.8 - - - +
38T LEU* 3.8 18.6 - - + -
39T THR* 3.0 15.5 - - - +
40T LEU* 3.3 18.2 - - + -
57T VAL* 4.8 7.0 - - + -
59T ILE* 5.9 4.7 - - + -
102T TYR* 5.0 0.2 + - - -
114T VAL 3.6 0.5 - - - +
115T TYR* 3.3 8.5 - - - +
116T TYR* 2.8 66.4 + - - +
118T PHE* 4.1 6.5 - - + -
122T LEU* 1.3 82.1 - - - +
124T ARG* 1.3 66.6 + - - +
125T LEU* 5.5 7.9 - - + -
142T LEU* 3.2 48.7 - - + -
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Residues in contact with ARG 124 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598M LEU* 3.3 22.2 - - + +
37T LYS* 6.5 0.2 - - - -
38T LEU* 2.9 24.4 + - - +
39T THR* 2.8 30.6 + - - -
105T GLU* 3.0 24.2 + - - -
107T VAL* 3.4 29.7 - - - +
113T ALA* 3.4 12.4 - - + +
114T VAL 3.4 7.2 - - - +
115T TYR* 3.5 27.1 + - + -
123T MET* 1.3 74.0 - - - +
125T LEU* 1.3 66.1 + - - +
126T GLU* 3.6 22.1 + - - -
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Residues in contact with LEU 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6T PHE* 3.8 31.2 - - + -
10T PHE* 4.2 20.6 - - + -
36T CYS* 4.5 1.1 - - - -
37T LYS 3.5 16.6 - - - +
38T LEU* 3.7 19.5 - - + -
57T VAL* 5.7 2.2 - - + -
59T ILE* 4.6 7.6 - - + -
113T ALA* 2.9 31.8 - - - +
114T VAL* 3.1 23.1 + - + +
116T TYR* 6.1 0.2 - - + -
123T MET* 5.5 9.9 - - + -
124T ARG* 1.3 73.6 - - - +
126T GLU* 1.3 75.5 + - - +
130T ARG* 4.4 6.3 - - - +
134T ASN* 3.9 22.4 - - - +
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Residues in contact with GLU 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T GLN 3.5 14.1 - - - +
36T CYS* 3.1 27.5 - - - -
37T LYS* 3.1 50.2 + - + +
107T VAL* 4.2 17.4 - - + +
111T LEU* 4.7 10.9 - - - +
112T ILE 3.2 9.6 - - - +
113T ALA* 3.7 12.3 - - + -
124T ARG* 3.6 30.5 + - - +
125T LEU* 1.3 86.5 - - - +
127T GLY* 1.3 58.8 + - - +
129T TYR* 3.9 0.5 + - - -
130T ARG* 3.8 10.5 + - - +
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Residues in contact with GLY 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T GLN* 3.9 25.6 + - - +
110T ASP 3.5 0.5 - - - +
111T LEU* 3.5 24.2 - - - +
112T ILE 3.4 6.2 + - - +
126T GLU* 1.3 78.2 - - - +
128T ASN* 1.3 68.5 + - - +
129T TYR* 3.9 15.0 - - - -
130T ARG* 4.3 0.9 - - - -
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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