Contacts of the strand formed by residues 123 - 128 (chain A) in PDB entry 4KAL
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 ARG 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ALA* 2.9 37.2 + - - +
32A ALA 4.0 2.2 + - - +
115A ILE* 3.7 16.4 - - + -
116A PHE 3.5 4.0 - - - +
117A VAL* 4.5 1.8 - - + -
122A GLU* 1.3 86.6 + - - +
124A SER* 1.3 63.5 + - - +
125A MSE 3.3 41.6 - - + +
156A TYR* 4.2 6.9 + - - -
186A SER 5.2 4.2 + - - -
187A ASP* 5.4 2.4 + - - -
270A ASP* 4.0 7.0 - - - +
271A THR* 3.5 21.1 + - - +
272A THR* 3.2 37.8 - - - +
273A GLY 5.0 0.6 - - - +
401A ADN 4.4 9.9 + - - -
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Residues in contact with SER 124 (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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23A LEU* 3.7 18.2 - - - +
28A ILE* 3.8 23.8 - - - -
29A THR 3.9 2.9 - - - -
30A LYS* 3.3 9.0 - - - +
31A ALA 3.0 23.1 + - - +
32A ALA 3.9 4.0 - - - -
115A ILE* 4.4 0.2 - - - -
116A PHE* 2.9 35.7 + - - -
118A THR* 5.5 0.9 + - - -
122A GLU* 5.0 1.0 - - - +
123A ARG* 1.3 75.7 + - - +
125A MSE 1.3 60.3 + - - +
126A ASN* 3.4 9.5 + - - -
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Residues in contact with MSE 125 (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 ALA 2.9 7.7 + - - +
33A MSE 3.7 12.8 - - + -
34A ASN* 2.8 33.4 + - - -
113A SER* 3.6 11.0 - - - +
114A MSE 3.6 3.6 - - - -
115A ILE* 3.8 16.6 - - + +
123A ARG* 3.3 45.1 - - + +
124A SER* 1.3 76.0 - - - +
126A ASN* 1.3 63.4 + - - +
127A THR* 4.1 1.1 - - - +
156A TYR* 3.3 20.9 - - - +
401A ADN 3.4 57.7 - - + +
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Residues in contact with ASN 126 (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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28A ILE* 3.6 25.1 - - - +
34A ASN* 3.2 24.0 - - - +
36A ILE* 3.6 18.7 - - + +
40A ARG* 4.8 1.6 + - - -
44A LEU* 3.8 28.7 - - + +
112A ARG 3.9 0.9 - - - +
113A SER* 3.3 2.1 + - - -
114A MSE 2.9 48.6 + - + +
116A PHE* 3.4 23.0 - - - -
124A SER 3.4 5.1 + - - -
125A MSE 1.3 77.8 - - - +
127A THR* 1.3 59.4 + - - +
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Residues in contact with THR 127 (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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11A ILE* 3.8 20.0 - - + -
33A MSE 3.8 16.1 - - - +
34A ASN 2.8 9.7 + - - -
35A LEU* 3.6 8.4 - - - +
36A ILE* 3.0 24.8 + - - +
112A ARG 3.6 9.2 - - - +
113A SER* 2.8 15.3 + - - -
126A ASN* 1.3 72.4 + - - +
128A TYR* 1.3 64.9 + - - +
129A LEU* 3.8 15.1 + - + -
401A ADN 2.7 39.8 + - - +
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Residues in contact with TYR 128 (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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36A ILE* 3.6 27.2 - - + +
37A ASP* 3.9 2.2 - - - -
38A ALA* 3.8 29.2 - - + +
41A ALA* 4.3 7.0 - - + -
108A PRO* 4.3 5.2 - - - +
109A PRO* 3.9 23.4 - - + +
110A THR 4.9 0.2 - - - -
111A ALA* 3.3 3.5 - - - +
112A ARG* 3.0 55.2 + - - +
126A ASN 4.0 0.6 + - - -
127A THR* 1.3 70.9 - - - +
129A LEU* 1.3 65.5 + - - +
130A GLY* 3.5 26.2 - - - -
404A DMS 3.8 31.6 - - + +
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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