Contacts of the strand formed by residues 86 - 95 (chain A) 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 GLY 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 5.0 2.4 - - - +
35A SER* 3.0 14.6 - - - -
37A THR* 3.6 11.2 - - - -
62A GLN* 3.8 9.4 + - - -
84A HIS 3.8 1.2 + - - -
85A PHE* 1.3 80.5 - - - +
87A HIS* 1.3 64.3 + - - +
254A PRO* 4.1 2.9 - - - +
255A VAL* 3.0 34.8 + - - +
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Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.7 9.4 - - + -
32A LYS* 4.3 33.9 + - + +
35A SER* 3.8 22.7 - - - -
37A THR* 3.3 12.7 - - - +
38A GLU* 3.2 38.8 + - - -
39A GLY 4.7 3.3 - - - +
40A GLY* 5.3 1.8 - - - -
42A LYS* 4.2 10.6 - - - -
86A GLY* 1.3 75.5 - - - +
88A ILE* 1.3 75.7 + - - +
89A GLU* 4.6 15.0 - - + -
252A VAL* 4.1 18.0 - - + +
253A LEU 3.4 10.8 - - - +
255A VAL* 4.0 5.0 - - - +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY* 6.0 3.8 - - - -
42A LYS* 4.1 14.8 - - - +
87A HIS* 1.3 82.4 - - - +
89A GLU* 1.3 62.5 + - - +
90A LEU* 3.7 23.1 + - + -
252A VAL* 3.4 4.5 - - - +
253A LEU* 2.8 51.9 + - + +
255A VAL* 3.6 22.0 - - + -
280A LEU* 3.8 16.6 - - + -
283A ILE* 4.9 4.7 - - + -
284A VAL* 3.7 27.8 - - + -
287A ASN* 4.0 16.6 - - + +
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Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 5.2 15.8 + - + +
40A GLY* 5.9 3.8 - - - -
87A HIS* 4.1 13.3 + - + -
88A ILE* 1.3 76.4 - - - +
90A LEU* 1.3 70.8 + - - +
251A THR 4.3 6.3 - - - +
252A VAL* 4.8 11.6 - - + +
287A ASN* 3.2 14.6 + - - -
291A ARG* 3.7 14.9 + - - +
227R SER* 4.7 10.4 + - - -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE* 3.9 17.7 - - + +
89A GLU* 1.3 76.8 - - - +
91A ALA* 1.3 57.9 + - - +
92A LYS* 3.5 14.6 - - - +
94A VAL* 3.8 29.4 - - + -
250A VAL* 3.8 19.7 - - + +
251A THR 3.3 20.5 + - - +
253A LEU* 4.7 19.3 - - + -
283A ILE* 4.9 2.0 - - + -
287A ASN* 3.2 20.6 - - + +
291A ARG* 2.5 24.2 + - - -
310A LEU* 4.4 16.6 - - + -
314A VAL* 5.0 5.2 - - + -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 1.3 74.8 - - - +
92A LYS* 1.3 69.1 + - + +
287A ASN* 2.9 19.0 + - - +
290A LEU* 3.6 38.8 - - + +
291A ARG* 3.6 30.8 + - - +
294A GLU* 4.1 9.8 - - - +
310A LEU* 4.9 0.6 - - - +
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 3.5 20.0 - - - +
91A ALA* 1.3 84.6 + - + +
93A PRO* 1.3 79.5 - - + +
94A VAL* 3.7 10.6 + - + +
219A GLU* 5.1 14.8 + - + +
290A LEU* 5.0 7.4 - - + +
294A GLU* 3.1 29.2 + - - +
303A ILE* 3.7 27.8 - - - -
307A VAL* 3.9 25.4 - - + -
310A LEU* 4.2 3.8 - - + +
67Q LYS* 5.9 2.8 - - - +
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Residues in contact with PRO 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LYS* 1.3 93.5 - - + +
94A VAL* 1.3 65.7 + - - +
218A PRO* 3.4 14.2 - - - +
219A GLU* 3.5 41.3 + - + -
222A HIS* 4.8 7.9 - - - +
249A ILE* 3.8 14.4 - - + -
250A VAL 3.6 7.6 - - - +
251A THR* 3.6 28.7 - - + -
307A VAL* 5.6 0.9 - - - +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 3.8 17.5 - - + -
92A LYS* 4.0 8.3 - - + +
93A PRO* 1.3 79.7 - - - +
95A PHE* 1.3 63.9 - - - +
218A PRO* 4.1 5.2 - - + -
249A ILE* 3.3 6.7 - - - +
250A VAL* 3.0 49.0 + - + +
307A VAL* 4.5 21.3 - - + -
310A LEU* 4.1 19.3 - - + -
311A GLN* 3.6 18.6 - - - +
314A VAL* 4.0 18.8 - - + -
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 1.3 77.5 - - - +
96A HIS* 1.3 60.3 + - - +
97A VAL* 3.9 1.0 + - - -
100A LEU* 4.0 25.1 - - + -
103A THR* 5.0 12.6 - - + -
196A LEU* 4.1 12.6 - - + -
197A GLU* 5.4 1.1 - - - -
198A LEU* 4.2 31.4 - - + -
216A LEU 4.2 8.3 - - - -
218A PRO* 3.3 39.9 - - + +
221A VAL* 3.9 24.7 - - + -
249A ILE* 4.3 20.4 - - + -
250A VAL* 4.2 2.3 - - - +
311A GLN* 2.8 48.2 + - - +
314A VAL* 4.4 3.6 - - - +
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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