Contacts of the strand formed by residues 131 - 139 (chain L) in PDB entry 3KC3
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 131 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273B PRO* 5.6 9.9 - - + -
277B THR* 5.3 6.9 + - - +
280B ARG* 5.9 1.1 - - - +
110J ARG* 4.6 4.0 - - - +
179J SER 3.5 8.3 + - - -
180J ILE* 3.2 31.6 + - - +
181J ASN* 2.3 28.6 + - - -
216J SER* 2.9 44.3 + - - +
96L GLN* 4.9 19.1 - - + +
127L LEU* 3.2 5.6 - - - +
128L TYR* 2.7 43.4 + - + +
129L ALA* 2.7 21.4 + - + +
130L GLY* 1.3 72.9 + - - -
132L LYS* 1.3 63.7 + - - +
133L CYS* 3.5 16.0 + - - -
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Residues in contact with LYS 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J GLU* 3.4 36.6 + - - +
110J ARG* 4.5 15.5 - - - +
96L GLN* 4.3 0.7 - - - +
97L ASP* 3.2 42.7 + - + +
102L ARG* 5.0 0.8 - - - +
125L GLU* 2.8 44.1 + - + +
126L ASN 4.1 5.4 - - - +
127L LEU* 3.6 14.5 - - + +
130L GLY 3.9 1.4 + - - -
131L ARG* 1.3 73.5 - - - +
133L CYS* 1.3 67.3 + - - +
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Residues in contact with CYS 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L MET* 6.0 0.9 - - + -
95L LEU 3.5 14.4 - - - +
96L GLN* 4.0 13.0 - - - -
97L ASP* 4.2 1.8 - - - +
124L TYR 3.4 1.4 - - - +
125L GLU* 3.3 5.9 - - - -
126L ASN* 2.7 45.3 + - + +
128L TYR* 4.6 20.4 - - + -
131L ARG* 3.5 27.1 + - - +
132L LYS* 1.3 87.3 - - - +
134L LEU* 1.3 65.3 + - - +
135L LEU* 3.8 11.2 + - + +
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Residues in contact with LEU 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L ILE* 4.7 7.2 - - + -
93L LYS 4.0 0.3 - - - +
94L MET* 3.6 2.3 - - - -
95L LEU* 2.9 39.5 + - + +
97L ASP* 3.7 12.5 - - + +
101L ALA* 3.5 44.9 - - + +
102L ARG* 3.6 38.1 - - + +
105L VAL* 4.3 15.5 - - + -
123L VAL* 4.6 13.2 - - + -
124L TYR 3.3 8.1 - - - +
125L GLU* 4.7 8.7 - - + -
133L CYS* 1.3 72.7 - - - +
135L LEU* 1.3 62.2 + - - +
136L ILE* 4.2 2.5 - - + +
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Residues in contact with LEU 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J PHE* 6.4 0.4 - - + -
48J VAL* 5.0 10.5 - - + -
59L ILE* 3.6 30.5 - - + -
92L LEU* 3.6 15.3 - - + -
93L LYS 3.5 2.2 - - - -
94L MET* 3.6 38.6 - - + -
122L ASP 3.9 0.2 - - - +
123L VAL* 3.4 4.9 - - - +
124L TYR* 2.8 48.1 + - + +
126L ASN* 3.6 23.8 - - + +
128L TYR* 5.9 3.8 - - + -
133L CYS* 4.3 16.4 - - + +
134L LEU* 1.3 77.9 - - - +
136L ILE* 1.3 62.6 + - - +
137L VAL 3.9 0.7 + - - -
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Residues in contact with ILE 136 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91L ALA 3.5 0.5 - - - +
92L LEU* 3.3 5.6 - - - +
93L LYS* 2.8 55.7 + - + +
95L LEU* 4.1 20.0 - - + -
104L GLU* 4.9 5.8 - - + +
105L VAL* 3.3 33.7 - - + -
108L HIS* 5.4 4.5 - - - +
120L ILE* 3.7 39.3 - - + -
122L ASP 3.8 1.6 - - - -
123L VAL* 4.2 9.0 - - + -
134L LEU* 4.8 2.2 - - + -
135L LEU* 1.3 78.1 - - - +
137L VAL* 1.3 64.0 - - - +
138L MET* 3.6 10.9 + - + +
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Residues in contact with VAL 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L ILE* 3.8 20.9 - - + -
63L TYR* 3.8 22.2 - - + +
81L ILE* 3.8 22.2 - - + -
90L PHE* 3.7 30.7 - - + -
91L ALA 3.2 7.4 - - - +
92L LEU* 4.5 1.3 - - + -
120L ILE* 3.6 3.8 - - - +
121L VAL* 2.7 40.7 + - + -
122L ASP* 2.9 21.6 + - + +
124L TYR* 4.2 7.6 - - + -
135L LEU 3.9 0.2 + - - -
136L ILE* 1.3 72.0 - - - +
138L MET* 1.3 55.6 + - - +
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Residues in contact with MET 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L VAL* 3.8 22.2 - - + -
90L PHE* 4.0 3.1 - - - -
91L ALA* 2.9 29.5 + - + +
92L LEU 4.3 0.4 - - - -
93L LYS* 3.3 39.5 - - + +
108L HIS* 4.3 11.0 - - - -
118L VAL* 4.0 9.4 - - + -
119L ARG 3.2 19.3 - - - +
120L ILE* 4.5 5.6 - - + -
121L VAL* 4.3 3.1 - - - -
136L ILE* 3.9 10.3 - - + +
137L VAL* 1.3 76.8 - - - +
139L GLU* 1.3 69.8 + - - +
500L MK2 3.3 41.5 - - + +
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Residues in contact with GLU 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90L PHE* 4.6 6.5 - - - -
91L ALA* 4.0 0.2 - - - +
118L VAL* 3.6 14.2 - - + +
119L ARG* 2.8 49.9 + - + +
121L VAL* 3.9 15.8 - - + +
138L MET* 1.3 74.8 - - - +
140L CYS* 1.3 62.6 + - - +
141L LEU* 3.8 15.0 - - + +
195L THR* 4.3 4.7 - - - +
204L LYS* 3.3 36.7 + - - +
500L MK2 3.5 17.5 + - - -
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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