Contacts of the strand formed by residues 86 - 93 (chain I) in PDB entry 5HHM
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 86 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37I ARG* 4.6 2.0 - - - -
38I GLN 3.5 10.8 - - - -
39I GLU* 5.0 2.9 - - - -
40I PRO* 5.8 2.9 - - - -
84I ASP 3.6 1.6 + - - -
85I THR* 1.3 76.4 - - - +
87I LEU* 1.3 63.2 + - - -
88I TYR* 3.5 10.1 - - - -
105I THR 3.4 2.1 - - - +
106I LYS* 4.5 5.8 - - - -
107I LEU 2.8 33.2 + - - -
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Residues in contact with LEU 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I GLN 5.6 0.2 - - - +
36I TYR 3.8 0.2 - - - +
37I ARG* 3.3 4.5 - - - +
38I GLN* 2.7 61.3 + - + +
86I GLY* 1.3 72.8 - - - -
88I TYR* 1.3 59.0 + - - +
89I LEU* 4.0 25.5 - - + +
103I LYS 4.2 5.6 - - - +
104I GLY* 3.8 8.7 - - - -
105I THR 3.4 30.3 - - - +
106I LYS* 4.0 12.3 - - + +
39J GLN* 4.4 1.6 - - - +
43J GLN 4.1 19.3 - - - +
44J GLY* 5.2 1.1 - - - -
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Residues in contact with TYR 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I GLN* 2.9 17.9 + - - -
22I VAL* 4.9 4.0 - - + -
35I TRP* 4.5 6.1 - - + -
36I TYR 3.2 4.5 - - - +
37I ARG* 3.5 30.6 - - + -
47I LEU* 4.0 10.5 - - + -
62I LEU* 3.9 22.8 - - + +
75I LEU* 3.5 27.6 - - + -
77I ILE* 3.9 8.8 - - + +
84I ASP* 2.6 49.4 + - - +
86I GLY 3.5 16.6 - - - -
87I LEU* 1.3 71.8 - - - +
89I LEU* 1.3 61.2 + - - +
104I GLY* 3.2 0.5 - - - -
105I THR* 3.0 33.0 + - + +
107I LEU* 3.6 17.5 - - + -
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Residues in contact with LEU 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I GLN* 3.4 6.3 - - - +
34I GLN 3.9 0.2 - - - +
35I TRP* 3.3 5.8 - - - -
36I TYR* 2.8 54.2 + - + +
38I GLN* 4.5 19.7 - - + +
44I PRO* 4.6 9.6 - - + -
87I LEU* 4.0 27.1 - - + -
88I TYR* 1.3 75.9 - - - +
90I CYS* 1.3 58.4 + - - +
101I PHE* 4.4 16.6 - - + -
102I GLY 3.5 20.6 - - - +
103I LYS* 4.1 3.1 - - - +
104I GLY* 3.8 14.1 - - - +
39J GLN* 5.8 0.4 - - - +
44J GLY* 5.2 7.4 - - - -
45J LEU* 4.9 17.5 - - + +
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Residues in contact with CYS 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I LEU* 4.2 10.0 - - - +
7I GLN* 3.0 23.8 + - - -
24I CYS* 2.0 53.6 - - + -
33I LEU* 4.3 3.1 - - + -
34I GLN 3.2 10.1 - - - +
35I TRP* 3.8 17.9 - - + -
89I LEU* 1.3 74.1 - - - +
91I ALA* 1.3 61.4 + - - +
100I ILE 4.1 0.2 - - - +
101I PHE* 3.8 2.8 - - - -
102I GLY* 3.0 26.2 + - - -
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Residues in contact with ALA 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I LEU* 4.0 4.7 - - - -
33I LEU* 3.3 5.7 - - - +
34I GLN* 2.7 41.7 + - + +
36I TYR* 4.4 6.3 - - + -
89I LEU 4.3 0.2 + - - -
90I CYS* 1.3 74.5 - - - +
92I GLY* 1.3 57.8 + - - +
99I LEU* 3.9 22.4 - - + -
100I ILE 3.1 12.8 - - - +
101I PHE* 3.7 26.5 - - + -
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Residues in contact with GLY 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I LEU* 3.6 4.8 - - - +
30I PHE* 3.6 18.6 - - - -
32I SER 3.4 11.2 - - - -
33I LEU* 4.3 2.0 - - - -
34I GLN* 4.6 0.7 - - - -
91I ALA* 1.3 74.7 - - - +
93I ALA* 1.3 64.1 + - - -
94I GLY 3.2 0.7 + - - -
99I LEU* 3.4 8.6 - - - -
100I ILE* 2.8 37.6 + - - +
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Residues in contact with ALA 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F GLN* 3.5 15.3 + - - +
3I GLN* 2.9 19.1 + - - -
30I PHE* 3.5 6.4 - - - -
31I SER* 3.3 28.9 - - - +
32I SER* 3.2 27.4 + - - +
34I GLN* 4.9 0.2 + - - -
92I GLY* 1.3 69.0 - - - -
94I GLY* 1.3 60.9 + - - +
95I SER 3.9 0.2 + - - -
99I LEU* 4.3 1.0 - - - +
98J ARG* 5.8 0.2 - - - +
100J SER 3.4 18.9 + - - +
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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