Contacts of the strand formed by residues 90 - 98 (chain H) in PDB entry 5IYB
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 90 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579A ILE* 4.6 4.9 - - + +
581A LYS* 3.9 14.3 - - - +
582A PRO* 4.6 6.7 - - + -
43H VAL* 3.7 8.2 - - + -
44H ASN* 3.0 30.2 + - + +
47H ILE* 4.2 17.3 - - + -
48H TYR* 3.9 42.6 - + + -
88H PHE 3.5 2.6 + - - -
89H GLU* 1.3 80.3 - - - +
91H VAL* 1.3 63.2 + - - +
92H MET* 3.2 46.4 - - + -
121H LEU* 4.5 0.5 - - - +
143H LEU* 4.3 1.8 - - + -
144H LEU* 3.4 2.3 - - - -
145H MET* 2.8 63.7 + - + +
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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
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579A ILE* 3.6 6.8 - - - +
580A LEU* 3.0 56.3 + - + -
581A LYS* 3.5 30.4 + - + +
64H LEU* 4.8 5.2 - - + -
85H ALA 4.3 15.9 - - - +
88H PHE* 4.9 2.7 - - + -
90H TYR* 1.3 81.2 - - - +
92H MET* 1.3 76.2 + - - +
142H TYR* 4.8 6.3 - - + -
143H LEU 3.1 7.2 - - - +
144H LEU* 4.3 17.7 - - + -
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Residues in contact with MET 92 (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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578A ALA* 3.3 15.5 - - - +
579A ILE* 4.6 6.5 - - + +
580A LEU* 4.7 1.3 - - - +
41H LEU* 4.2 2.2 - - + -
42H ASP 4.0 17.9 - - - +
90H TYR* 3.2 37.0 - - + +
91H VAL* 1.3 84.2 - - - +
93H TYR* 1.3 60.5 + - - +
118H TYR* 4.0 34.8 - - + -
121H LEU* 3.9 19.5 - - + -
142H TYR* 3.3 4.9 - - - +
143H LEU* 2.5 67.4 + - + +
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Residues in contact with TYR 93 (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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576A GLN* 3.6 41.1 - - + -
577A PRO 3.9 13.4 + - - +
578A ALA* 3.2 13.3 + - - +
580A LEU* 5.2 3.3 - - + +
590A GLN* 4.9 5.5 + - - -
70H LEU* 5.8 1.6 - - + -
73H GLY* 5.9 2.9 - - - -
92H MET* 1.3 73.6 - - - +
94H GLY* 1.3 67.7 + - - +
95H LYS* 5.5 4.4 - - - -
118H TYR* 3.4 22.3 - - - +
119H GLY 4.2 1.0 + - - -
139H SER* 2.4 33.8 + - - -
140H ARG* 4.1 5.8 - - - -
141H VAL 3.0 24.7 - - - -
142H TYR* 3.7 35.4 - + + -
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Residues in contact with GLY 94 (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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93H TYR* 1.3 86.8 - - - +
95H LYS* 1.3 62.7 + - - +
116H VAL* 4.6 0.7 - - - -
117H SER 3.2 13.9 - - - -
118H TYR* 3.4 11.1 - - - -
119H GLY 5.0 0.9 - - - -
139H SER 4.0 0.2 - - - -
140H ARG 3.8 2.8 + - - -
141H VAL* 2.9 36.5 + - - +
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Residues in contact with LYS 95 (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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632A ASN* 4.9 8.9 - - - +
634A GLU* 3.0 35.9 + - - +
636A ILE* 5.4 13.9 - - + -
93H TYR* 5.5 4.9 + - - -
94H GLY* 1.3 73.7 - - - -
96H VAL* 1.3 61.5 + - - +
97H TYR* 3.6 5.2 + - + +
116H VAL* 3.3 6.9 - - - +
117H SER* 2.9 37.0 + - - +
138H ASP 3.0 24.4 + - - +
139H SER* 3.3 32.7 - - - +
141H VAL* 4.6 2.7 - - - -
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Residues in contact with VAL 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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95H LYS* 1.3 76.7 - - - +
97H TYR* 1.3 59.1 + - - +
98H ARG 3.3 16.2 - - - +
99H ILE* 4.1 15.0 - - + -
114H ALA* 4.7 6.3 - - + -
115H TYR 3.1 22.0 - - - +
116H VAL* 4.0 13.5 - - + -
135H PHE 5.0 4.3 - - - +
136H GLU* 5.1 1.8 - - - -
137H VAL* 3.1 36.5 + - + +
138H ASP* 4.2 8.0 - - - +
141H VAL* 3.6 24.2 - - + +
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Residues in contact with TYR 97 (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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623A PRO* 4.0 15.9 - - - +
629A VAL* 5.4 6.3 - - + -
631A GLU* 4.2 16.1 - - - +
636A ILE* 3.8 33.2 - - + -
637A MET* 3.8 26.1 - - - -
95H LYS* 4.4 4.5 - - + +
96H VAL* 1.3 74.3 - - - +
98H ARG* 1.3 87.1 + - + +
115H TYR* 3.2 18.6 + + + +
116H VAL 3.8 17.7 - - - -
117H SER* 3.6 35.9 - - - -
122H LEU* 3.7 15.8 - - + +
123H MET 5.4 0.5 + - - -
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Residues in contact with ARG 98 (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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621A ILE* 5.8 4.4 - - - +
96H VAL* 3.3 6.1 - - - +
97H TYR* 1.3 99.5 - - + +
99H ILE* 1.3 71.3 + - - +
100H GLU* 3.4 27.7 + - - +
115H TYR* 3.1 60.9 + - + -
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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