Contacts of the strand formed by residues 109 - 114 (chain S) 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 LYS 109 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99S LEU* 5.9 1.3 - - + -
100S LEU 3.5 6.7 - - - +
101S ARG* 4.4 27.4 - - + -
104S GLY 4.1 16.2 - - - +
105S LYS* 4.4 20.9 + - - +
107S GLY 3.9 2.8 + - - +
108S ARG* 1.3 78.8 - - - +
110S PHE* 1.3 67.8 + - - +
149S LEU* 3.0 48.4 + - + +
150S ALA 4.5 16.3 + - - +
151S ARG* 4.6 17.0 - - - +
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Residues in contact with PHE 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S PHE* 4.4 13.7 - + - -
35S ASP* 4.1 7.4 - - - -
37S VAL* 5.3 4.5 - - + -
42S TRP* 4.2 26.5 - + - -
99S LEU* 3.8 5.7 - - - +
100S LEU* 2.8 66.9 + - + +
102S VAL* 4.5 7.4 - - + -
108S ARG* 3.4 62.1 - - + -
109S LYS* 1.3 82.9 - - - +
111S LYS* 1.3 56.9 + - - +
146S PHE* 4.7 6.1 - - + -
147S THR* 3.3 15.3 - - - +
148S PRO* 3.4 17.0 - - + -
149S LEU* 4.1 5.6 - - - +
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Residues in contact with LYS 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLN* 4.8 11.5 + - - -
50S ASP* 4.2 20.6 - - - +
52S SER* 4.9 8.0 + - - -
97S PRO* 4.9 8.3 - - + -
98S TRP 3.5 10.5 - - - +
99S LEU* 4.7 1.8 - - + +
110S PHE* 1.3 74.8 - - - +
112S GLY* 1.3 65.3 + - - +
113S ILE* 4.0 11.0 + - + +
145S ASN 3.4 3.6 - - - +
146S PHE* 4.4 2.0 - - - -
147S THR* 3.0 41.6 + - - +
149S LEU* 3.6 36.1 - - + +
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Residues in contact with GLY 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97S PRO* 3.2 8.3 - - - +
98S TRP* 2.5 49.7 + - - +
100S LEU* 5.2 0.8 - - - +
111S LYS* 1.3 71.6 - - - +
113S ILE* 1.3 63.3 + - - -
114S LYS 4.2 0.2 + - - -
144S TYR* 5.2 0.2 - - - -
146S PHE* 3.4 31.9 - - - -
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Residues in contact with ILE 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B PHE* 6.3 3.1 - - + -
355B ASP* 6.0 2.0 - - - +
359B THR* 3.8 25.8 - - + +
97S PRO* 4.5 16.4 - - + -
111S LYS* 5.1 13.0 - - + +
112S GLY* 1.3 76.9 - - - +
114S LYS* 1.3 67.2 + - - +
144S TYR* 3.5 3.2 - - - -
145S ASN* 2.8 60.1 + - + +
147S THR* 5.7 9.0 - - + +
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Residues in contact with LYS 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ASP* 5.5 2.6 - - - +
356B PHE* 3.9 30.1 - - + -
94S GLU 5.4 6.9 + - - +
96S GLN 6.1 1.8 - - - +
97S PRO* 5.3 4.9 - - + +
98S TRP* 5.9 0.2 - - - -
112S GLY 4.2 0.8 + - - -
113S ILE* 1.3 78.0 - - - +
115S LYS* 1.3 75.3 + - + +
116S GLY* 3.0 6.2 + - - -
142S ASN* 3.2 25.0 + - + +
143S TRP 4.5 0.9 - - - +
144S TYR* 3.6 27.7 - - + +
145S ASN* 5.0 1.7 + - - -
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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