Contacts of the strand formed by residues 109 - 115 (chain A) in PDB entry 5KJH
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 PRO 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A TYR* 3.5 29.6 - - + +
100A TRP* 3.9 6.1 - - + -
101A SER 3.9 2.2 - - - +
107A ASP 3.9 0.6 - - - +
108A GLN* 1.4 90.1 - - + +
110A LEU* 1.4 63.7 + - - +
111A LEU 4.2 0.4 - - - -
124A ASN* 4.2 1.6 - - - +
125A VAL* 3.7 20.2 + - + +
126A THR* 4.0 14.0 + - + -
243B PRO* 3.6 33.0 - - + -
244B PHE* 3.5 31.9 - - + -
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Residues in contact with LEU 110 (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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100A TRP* 3.4 8.3 - - - -
101A SER* 2.8 43.6 + - - +
102A LYS 3.6 7.6 - - - +
103A ASP* 3.5 36.8 - - + +
104A PRO* 4.9 0.7 - - + -
108A GLN* 4.5 3.4 - - + +
109A PRO* 1.4 78.2 - - - +
111A LEU* 1.3 60.6 + - - +
112A CYS 4.0 0.3 + - - -
122A VAL* 3.8 15.7 - - + -
123A TYR 3.4 12.1 - - - +
124A ASN* 4.0 9.4 - - + -
131A TYR* 3.8 51.1 - - + -
168A LEU* 4.0 9.0 - - + -
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Residues in contact with LEU 111 (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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44A LYS* 5.7 0.2 - - + -
58A ALA* 3.8 32.8 - - + -
60A THR* 5.2 0.2 - - - +
65A ALA* 3.8 19.1 - - + -
67A ILE* 4.4 2.2 - - + -
98A SER* 4.3 11.7 - - - +
99A CYS 3.8 13.9 - - - +
100A TRP* 3.9 22.6 - - + +
109A PRO 4.2 0.6 - - - -
110A LEU* 1.3 73.4 - - - +
112A CYS* 1.4 62.3 + - - +
113A ILE* 3.7 23.3 - - + -
121A LYS 3.5 2.4 - - - +
122A VAL* 4.4 0.4 - - - -
123A TYR* 2.8 44.4 + - + -
125A VAL* 3.6 27.3 - - + +
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Residues in contact with CYS 112 (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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98A SER* 3.0 28.2 - - - -
99A CYS* 2.9 32.4 + - - +
101A SER* 4.4 10.1 - - - -
110A LEU 4.7 0.2 - - - -
111A LEU* 1.4 71.2 - - - +
113A ILE* 1.3 61.4 + - - +
120A VAL* 3.7 19.1 - - + -
121A LYS 3.1 5.8 - - - +
122A VAL* 4.0 23.6 - - - -
134A LEU* 5.7 0.2 - - - -
144A LEU* 4.0 3.4 - - + -
154A ILE* 3.9 28.9 - - - -
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Residues in contact with ILE 113 (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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60A THR* 3.3 32.1 - - + +
64A HIS 6.5 0.7 - - - -
65A ALA* 4.5 7.4 - - + -
89A ASP* 5.8 0.7 - - + -
95A ASN* 3.4 36.8 - - + +
97A ALA 3.3 3.4 - - - +
98A SER* 3.5 9.2 - - - -
111A LEU* 3.7 20.6 - - + -
112A CYS* 1.3 83.9 - - - +
114A ALA* 1.3 64.7 + - - +
120A VAL* 3.7 0.2 - - - -
121A LYS* 2.7 46.2 + - - +
123A TYR* 3.8 32.3 - - + +
144A LEU* 4.2 0.9 - - - -
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Residues in contact with ALA 114 (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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95A ASN* 3.4 8.7 - - - +
96A CYS 3.0 22.2 + - - -
97A ALA* 2.9 19.1 + - + +
113A ILE* 1.3 75.6 - - - +
115A GLY* 1.3 58.2 + - - +
119A ASN 3.7 14.8 - - - +
120A VAL* 4.3 4.3 - - + -
121A LYS* 4.3 0.2 - - - +
141A ILE* 3.6 33.4 - - + -
144A LEU* 3.8 14.6 - - + -
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Residues in contact with GLY 115 (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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93A GLU* 3.8 5.6 + - - -
94A ALA 3.3 14.8 - - - -
95A ASN* 3.4 9.5 + - - -
96A CYS* 4.2 3.6 - - - -
114A ALA* 1.3 76.4 - - - +
116A ASN* 1.4 61.4 + - - -
117A GLU 3.2 4.8 + - - -
118A GLY 3.3 5.5 + - - -
119A ASN 4.4 2.2 + - - -
141A ILE* 2.8 37.3 + - - +
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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