Contacts of the strand formed by residues 134 - 142 (chain A) in PDB entry 3K5M
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 THR 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLN* 3.5 37.0 - - + +
35A THR* 5.8 1.3 - - - -
130A MET* 3.5 5.2 - - - +
131A HIS* 2.6 47.4 + - + +
132A ASN 3.8 7.6 - - - +
133A GLY* 1.3 84.8 - - - +
135A ILE* 1.3 66.6 + - - +
136A VAL* 3.8 15.3 - - - +
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Residues in contact with ILE 135 (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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1A MET* 3.4 38.1 - - + +
32A LEU* 3.4 35.4 - - + -
33A GLN 3.0 5.3 + - - +
34A VAL* 3.5 15.7 - - + -
35A THR* 2.6 33.6 + - - -
126A VAL* 4.6 5.6 - - + -
127A GLU 4.4 2.5 - - - +
128A GLY* 3.8 27.8 - - - +
129A ASP 3.6 2.0 - - - +
130A MET* 4.8 4.3 - - - -
133A GLY 5.6 0.4 - - - -
134A THR* 1.3 80.2 + - - +
136A VAL* 1.3 63.8 + - - +
138A ALA* 3.8 19.3 - - + -
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Residues in contact with VAL 136 (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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35A THR* 3.2 16.2 - - + +
128A GLY* 3.9 0.3 - - - -
129A ASP* 3.0 44.0 + - + +
131A HIS* 3.9 25.1 - - + -
134A THR* 3.8 16.2 - - - +
135A ILE* 1.3 79.4 - - - +
137A ASN* 1.3 75.1 + - + +
138A ALA 3.0 2.3 + - - -
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Residues in contact with ASN 137 (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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35A THR 2.9 6.2 + - - -
36A LEU 4.3 2.0 + - - -
37A ALA* 4.0 33.3 - - - +
38A PRO* 5.1 3.2 - - - +
127A GLU 4.1 0.2 - - - +
128A GLY* 4.0 8.5 - - - -
129A ASP* 3.7 17.4 - - - +
136A VAL* 1.3 80.7 - - + +
138A ALA* 1.3 64.5 + - - +
139A ARG* 3.9 6.1 + - - -
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Residues in contact with ALA 138 (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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34A VAL* 3.6 28.0 - - + -
35A THR 2.9 15.8 + - - +
36A LEU* 3.5 22.3 - - + +
37A ALA* 4.0 2.6 + - - +
114A TYR* 4.5 1.4 + - - -
126A VAL* 4.0 4.5 - - + -
127A GLU 3.2 12.1 - - - +
135A ILE* 3.8 15.5 - - + -
136A VAL 3.0 1.7 - - - -
137A ASN* 1.3 81.5 - - - +
139A ARG* 1.3 61.3 + - - +
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Residues in contact with ARG 139 (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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0A HIS* 4.1 12.7 + - - -
114A TYR* 3.4 11.9 - - - +
125A TRP 3.7 0.5 - - - +
126A VAL* 3.5 1.0 - - - +
127A GLU* 3.0 75.8 + - + +
128A GLY* 5.5 0.6 - - - -
137A ASN 4.9 4.9 - - - -
138A ALA* 1.3 75.6 - - - +
140A LEU* 1.3 70.3 + - - +
141A LYS* 5.8 6.7 - - + +
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Residues in contact with LEU 140 (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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7A ILE* 4.7 3.6 - - + -
23A PHE* 4.0 20.2 - - + -
25A LEU* 5.0 3.1 - - + -
34A VAL* 4.3 12.8 - - + -
36A LEU* 4.4 3.6 - - + -
114A TYR* 3.0 21.8 + - + -
115A LEU* 3.9 26.7 - - + -
118A ARG* 3.7 23.2 - - - +
120A ILE* 3.7 11.2 - - + +
124A VAL* 4.3 20.6 - - + -
125A TRP 3.4 4.7 - - - +
126A VAL* 3.4 35.7 - - + -
139A ARG* 1.3 76.7 - - - +
141A LYS* 1.3 65.7 - - - +
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Residues in contact with LYS 141 (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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120A ILE* 4.0 4.5 - - - -
124A VAL* 3.2 4.9 - - - +
125A TRP* 2.9 54.2 + - + +
127A GLU* 5.2 8.6 + - - -
139A ARG* 5.8 6.7 - - + +
140A LEU* 1.3 77.6 - - - +
142A PRO* 1.3 74.9 - - + +
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Residues in contact with PRO 142 (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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118A ARG* 3.6 25.4 - - + +
119A PHE* 3.8 20.9 - - + +
120A ILE* 3.6 12.5 - - + -
123A PRO 3.7 7.6 - - - +
125A TRP* 5.3 1.2 - - - +
140A LEU 4.8 0.2 - - - +
141A LYS* 1.3 91.0 - - + +
143A HIS* 1.3 58.7 + - - +
144A PRO* 3.4 13.5 - - + +
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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