Contacts of the strand formed by residues 87 - 98 (chain H) in PDB entry 3IT8
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 TYR 87 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H ALA* 3.1 19.0 + - + +
85H VAL 3.3 0.8 - - - -
86H SER* 1.3 80.3 - - - +
88H GLN* 1.3 52.5 + - - +
89H THR* 2.6 44.9 + - - +
91H VAL* 4.3 4.3 - - + -
58L HIS* 2.8 37.1 + + - +
153L ALA 5.5 1.1 - - - -
157L GLY* 3.5 25.4 - - - +
158L PHE* 4.7 0.9 - - - -
160L TYR* 4.2 14.8 - - + -
161L MET* 4.1 19.5 - - + -
162L GLY* 3.5 28.1 - - - -
165L LEU* 4.1 10.8 - - + -
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Residues in contact with GLN 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H ILE* 3.4 24.5 - - + -
84H ALA 3.3 6.0 + - - -
85H VAL* 3.0 31.9 + - - +
86H SER 4.4 0.4 - - - -
87H TYR* 1.3 65.1 - - - +
89H THR* 1.3 67.5 + - - +
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Residues in contact with THR 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H ARG 3.1 13.0 - - - +
83H ILE* 3.6 9.1 - - - +
84H ALA 4.5 0.3 + - - -
87H TYR* 2.6 38.4 + - - +
88H GLN* 1.3 81.9 + - - +
90H LYS* 1.3 78.1 + - - +
91H VAL* 3.1 8.2 + - + +
58L HIS* 4.6 15.9 - - + -
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Residues in contact with LYS 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H GLN* 4.0 17.2 - - - +
81H SER* 3.9 21.5 - - - +
82H ARG 3.6 5.8 - - - -
83H ILE* 4.2 12.5 - - + +
89H THR* 1.3 81.9 - - + +
91H VAL* 1.3 61.5 + - - +
92H ASN* 5.2 2.0 - - - +
133H SER* 4.0 9.2 - - - -
135H GLU* 3.1 40.0 + - - +
58L HIS* 5.2 2.6 - - - -
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Residues in contact with VAL 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H SER* 4.3 0.9 - - - -
82H ARG* 2.9 49.6 + - + +
84H ALA* 5.8 1.1 - - + +
87H TYR* 4.3 9.0 - - + -
89H THR 3.6 9.2 - - - +
90H LYS* 1.3 78.4 - - - +
92H ASN* 1.3 66.0 + - - +
93H LEU* 3.5 0.6 + - + -
34I ASN* 3.9 23.1 - - - +
58L HIS* 4.7 4.7 - - + -
161L MET* 4.0 15.0 - - - -
165L LEU* 3.7 31.4 - - + -
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Residues in contact with ASN 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H THR* 3.5 19.6 + - - +
80H ILE 3.9 3.4 - - - +
81H SER* 3.1 18.8 + - - -
90H LYS* 5.2 2.1 - - - +
91H VAL* 1.3 73.1 + - - +
93H LEU* 1.3 64.6 + - - +
94H LEU 4.9 4.5 - - - +
95H SER* 4.7 5.1 + - - -
34I ASN* 4.8 4.7 + - - +
146I GLU* 2.7 36.2 + - - +
147I SER* 4.2 14.1 + - - -
148I GLY 4.7 1.9 + - - +
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Residues in contact with LEU 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H ILE* 3.9 28.0 - - + -
80H ILE* 2.9 15.9 + - + +
81H SER 4.7 1.6 - - - -
82H ARG* 3.7 35.2 - - + +
91H VAL 4.2 1.3 - - - +
92H ASN* 1.3 76.8 - - - +
94H LEU* 1.3 73.0 + - + +
124H PHE* 3.6 33.2 - - + -
126H LEU* 5.1 0.4 - - + -
132H LEU* 4.1 6.1 - - + -
15I HIS* 4.9 2.8 + - - -
34I ASN* 3.5 43.7 - - + +
148I GLY* 3.5 15.9 - - - -
151I TYR* 5.1 0.2 - - - -
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Residues in contact with LEU 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H ILE* 4.0 7.0 - - + +
79H THR* 3.2 1.9 + - - -
80H ILE* 2.8 54.0 + - + +
92H ASN* 4.9 0.4 - - - +
93H LEU* 1.3 88.8 + - + +
95H SER* 1.3 64.7 + - - +
120H LEU* 3.7 16.2 - - + -
121H GLY* 3.6 29.2 - - - +
122H GLY* 3.7 5.6 - - - +
124H PHE* 3.7 26.5 - - + -
148I GLY* 3.5 5.4 - - - +
151I TYR* 3.4 39.3 - - + +
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Residues in contact with SER 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H THR* 5.5 1.6 - - - -
78H HIS 3.3 10.8 + - - -
79H THR* 3.6 16.4 - - - +
92H ASN* 4.7 4.2 + - - -
94H LEU* 1.3 77.1 - - - +
96H ALA* 1.3 68.5 + - - +
97H ILE* 5.1 2.8 - - - +
120H LEU* 4.0 6.2 - - - +
61I GLN* 3.4 4.5 - - - +
63I LEU* 5.1 0.2 - - - +
146I GLU* 3.9 29.8 + - - +
148I GLY 2.9 17.0 + - - +
149I GLN* 3.4 21.0 + - - +
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Residues in contact with ALA 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77H THR* 3.4 4.7 - - - -
78H HIS 3.0 30.0 + - - +
95H SER* 1.3 76.4 + - - +
97H ILE* 1.3 68.2 + - - +
118H ILE* 3.8 18.7 - - + +
120H LEU* 3.7 18.8 - - + +
61I GLN* 4.1 9.9 - - - +
63I LEU* 4.8 6.7 - - + -
117I PRO* 4.2 16.6 - - + -
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Residues in contact with ILE 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H LEU* 4.4 18.4 - - + -
76H LEU 3.3 11.2 - - - +
77H THR* 4.2 18.2 - - + -
95H SER* 5.1 3.1 - - - +
96H ALA* 1.3 80.5 - - - +
98H LYS* 1.3 67.1 + - - +
118H ILE* 4.7 2.0 - - - -
63I LEU* 4.3 8.8 - - + +
115I TYR* 3.5 55.3 - - + +
117I PRO* 3.6 16.3 - - - +
143I LEU* 4.8 1.1 - - + -
149I GLN* 3.6 25.8 - - - +
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Residues in contact with LYS 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G LYS* 3.5 23.6 - - - +
75H LEU* 3.9 1.3 - - - -
76H LEU* 2.8 38.9 + - + +
97H ILE* 1.3 80.7 - - - +
99H SER* 1.3 62.3 - - - +
100H PRO* 3.3 5.5 - - - +
116H GLU* 3.1 45.9 + - + +
117H PRO* 2.9 29.2 + - - +
118H ILE* 4.0 19.5 - - + -
98I LYS* 3.6 19.2 - - - +
115I TYR* 4.2 7.6 - - - +
116I GLU* 3.8 8.1 - - - +
117I PRO* 4.3 13.4 - - + +
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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