Contacts of the strand formed by residues 137 - 147 (chain K) in PDB entry 5D4C
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 137 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59K GLU* 4.7 17.8 + - - -
60K ASP* 4.8 10.7 + - - -
68K ILE* 3.9 21.0 - - - +
69K PRO 4.1 4.4 + - - -
71K VAL* 4.5 0.9 - - - +
103K ALA 3.7 4.7 - - - +
104K GLU* 3.6 31.8 + - + +
132K LEU* 3.6 2.9 - - - +
135K GLY* 3.4 13.6 + - - +
136K GLY* 1.3 75.3 - - - -
138K LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K ILE* 3.8 17.9 - - + -
68K ILE* 4.0 15.5 - - + -
71K VAL* 5.2 2.7 - - + -
78K ILE* 5.0 4.3 - - + -
101K LEU* 3.5 15.5 - - + +
102K LYS* 3.5 2.0 - - - +
103K ALA* 2.9 41.6 + - + +
109K VAL* 4.8 3.4 - - + -
129K ILE* 4.9 2.9 - - + -
130K ALA* 4.1 15.9 - - + -
132K LEU* 3.5 30.5 - - + +
137K ARG* 1.3 75.6 - - - +
139K ASN* 1.3 61.2 + - - +
140K MET* 3.6 46.4 - - + -
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Residues in contact with ASN 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K TYR* 3.8 5.6 - - - +
58K ILE* 3.3 6.7 - - - +
59K GLU* 3.0 58.3 + - + +
100K LEU* 6.0 1.0 - - - +
101K LEU 3.3 6.3 + - - +
102K LYS* 3.2 40.1 - - + +
138K LEU* 1.3 76.9 - - - +
140K MET* 1.3 68.9 + - - +
141K GLU* 5.2 7.3 + - - +
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Residues in contact with MET 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K VAL* 5.0 0.4 - - + -
57K TYR 3.1 6.7 - - - +
58K ILE* 3.8 19.5 - - + -
78K ILE* 4.2 7.9 - - - -
82K LEU* 4.2 21.8 - - + -
99K LEU 3.6 0.7 - - - +
100K LEU* 3.5 4.3 - - - -
101K LEU* 2.9 67.4 + - + +
114K PHE* 4.1 12.7 - - + -
129K ILE* 4.1 11.7 - - + -
138K LEU* 3.6 37.0 - - + -
139K ASN* 1.3 81.7 + - - +
141K GLU* 1.3 64.9 + - - +
142K VAL* 4.0 7.9 - - + -
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Residues in contact with GLU 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K SER 4.6 0.2 - - - -
56K VAL* 3.7 1.2 - - - -
57K TYR* 2.9 48.7 + - + +
98K THR* 4.0 18.4 - - + +
99K LEU 3.4 5.2 - - - -
100K LEU* 3.8 20.2 - - + +
139K ASN* 5.2 7.8 + - - +
140K MET* 1.3 76.3 - - - +
142K VAL* 1.3 62.3 + - - +
143K ARG 3.9 1.4 + - - -
160K ASP* 5.6 4.0 - - - +
161K ARG* 3.6 35.2 + - - -
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Residues in contact with VAL 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K VAL* 3.9 12.6 - - + -
55K SER 3.3 7.9 - - - +
56K VAL* 3.7 14.6 - - + -
82K LEU* 3.7 29.8 - - + -
85K LEU* 4.9 4.3 - - + -
97K VAL 3.5 1.4 - - - +
98K THR* 3.4 3.2 - - - -
99K LEU* 2.9 50.6 + - + +
114K PHE* 3.5 32.5 - - + -
140K MET* 4.5 11.4 - - + -
141K GLU* 1.3 75.3 - - - +
143K ARG* 1.3 59.9 + - - +
144K VAL* 3.6 6.5 + - + +
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Residues in contact with ARG 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K VAL* 3.5 1.6 - - - +
54K THR* 2.7 33.1 + - - +
55K SER* 2.9 25.3 + - - -
96K THR* 3.9 19.2 + - - +
97K VAL 3.7 3.8 - - - +
98K THR* 4.5 6.3 - - + +
141K GLU 3.9 2.0 + - - -
142K VAL* 1.3 70.3 - - - +
144K VAL* 1.3 54.9 + - - +
145K ASP* 2.7 36.6 + - - +
158K ILE* 3.6 32.0 - - - +
159K LYS 5.4 1.6 + - - -
160K ASP* 3.0 39.9 + - - +
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Residues in contact with VAL 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K THR* 4.2 8.3 - - - -
52K ALA 3.5 15.7 - - - +
53K VAL* 3.8 26.0 - - + -
85K LEU* 4.7 0.9 - - + -
87K VAL* 4.0 26.0 - - + -
89K PHE* 3.8 19.6 - - + -
96K THR* 3.3 4.5 + - - -
97K VAL 2.9 36.9 + - - +
99K LEU* 3.9 22.0 - - + -
142K VAL* 4.2 7.0 - - + +
143K ARG* 1.3 76.1 - - - +
145K ASP* 1.3 62.0 + - - +
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Residues in contact with ASP 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K THR* 3.3 9.8 - - - -
52K ALA 3.1 30.2 + - - +
54K THR* 2.8 30.0 + - + +
89K PHE* 4.5 0.9 - - - -
95K GLN* 3.4 7.3 - - - +
96K THR* 3.3 17.4 - - - +
143K ARG* 2.7 45.5 + - - +
144K VAL* 1.3 74.2 - - - +
146K ARG* 1.3 70.1 + - - +
158K ILE* 4.9 4.3 - - + -
171K PHE* 3.7 4.4 - - + -
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Residues in contact with ARG 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K PRO* 5.9 4.4 - - - +
50K GLY* 3.5 11.2 + - - +
51K THR* 4.0 9.0 - - + +
89K PHE* 3.5 34.3 + - + +
91K ASN 3.1 23.6 + - - -
92K PRO* 3.7 17.3 + - - +
94K LEU 2.9 28.4 + - - +
95K GLN* 2.9 42.5 + - - +
145K ASP* 1.3 81.1 - - - +
147K GLY* 1.3 59.4 + - - +
171K PHE* 4.0 2.8 - - - -
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Residues in contact with GLY 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K PRO* 3.4 6.2 - - - +
50K GLY 3.0 32.5 + - - +
146K ARG* 1.3 75.9 - - - +
148K VAL* 1.3 61.5 + - - -
171K PHE* 3.3 24.7 - - - +
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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