Contacts of the strand formed by residues 137 - 147 (chain B) in PDB entry 1TJJ
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 GLY 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B LYS* 4.0 9.6 - - - -
135B THR 3.4 1.6 + - - -
136B THR* 1.3 79.9 - - - +
138B ASN* 1.3 66.2 + - - +
139B TYR* 3.6 7.7 - - - -
160B SER* 3.4 3.3 - - - -
161B LEU 2.8 35.3 + - - +
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Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B SER* 3.3 26.7 + - - +
59B LYS* 3.4 7.1 - - - +
60B GLU* 2.7 59.5 + - + +
65B TRP* 3.4 12.9 - - + -
137B GLY* 1.3 76.2 - - - -
139B TYR* 1.3 61.6 + - - +
159B ALA 3.9 3.1 - - - +
160B SER* 2.7 27.8 + - - +
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Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU* 4.5 2.2 - - + -
58B GLU 3.3 15.7 - - - +
59B LYS* 3.5 27.1 - - + +
65B TRP* 3.7 6.8 - - - -
68B ILE* 4.0 8.7 - - + -
134B LEU 3.2 15.9 + - - -
135B THR* 2.7 33.2 + - - -
137B GLY* 3.6 20.0 - - - -
138B ASN* 1.3 77.6 - - - +
140B ARG* 1.3 61.9 + - - +
158B ALA* 3.4 5.9 - - - +
159B ALA 2.9 34.3 + - - +
161B LEU* 3.7 20.2 - - + -
2484B PFS 3.0 61.5 - - - +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL 3.7 0.9 - - - +
57B LEU* 3.4 4.7 - - - +
58B GLU* 2.9 49.0 + - - +
65B TRP* 3.4 60.5 - - + +
139B TYR* 1.3 78.2 - - - +
141B ILE* 1.3 60.2 + - - +
157B ILE 3.3 9.4 - - - +
158B ALA* 4.4 11.8 - - + +
2484B PFS 3.3 4.7 - - - -
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 4.4 26.7 - - + -
56B VAL 3.2 12.1 - - - +
57B LEU* 4.1 18.4 - - + -
75B GLY 5.3 2.0 - - - +
140B ARG* 1.3 76.0 - - - +
142B GLU* 1.3 70.9 + - - +
143B SER* 5.0 2.7 - - - +
155B ILE 4.0 0.3 - - - +
156B LYS* 3.2 4.6 - - - +
157B ILE* 2.8 63.3 + - + -
2484B PFS 3.8 26.0 - - + +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B CYS* 5.0 0.2 - - - +
54B ASP 3.7 1.2 - - - +
55B LEU* 3.3 3.8 - - - -
56B VAL* 2.9 56.5 + - + +
141B ILE* 1.3 76.9 - - - +
143B SER* 1.3 63.8 + - - +
144B VAL* 4.0 13.4 - - + +
151B ARG* 5.4 1.0 + - - -
154B CYS* 3.9 20.4 - - - -
155B ILE 3.4 10.3 - - - +
156B LYS* 2.7 38.2 + - + +
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 3.9 4.0 - - - +
54B ASP 3.5 3.8 - - - -
55B LEU* 3.0 26.7 - - - +
141B ILE* 4.2 4.0 - - - +
142B GLU* 1.3 73.2 - - - +
144B VAL* 1.3 60.0 + - - +
154B CYS* 3.2 2.4 - - - -
155B ILE* 2.9 39.0 + - - -
2485B LPE 2.6 51.0 + - - -
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS 3.5 1.6 - - - +
53B VAL* 3.4 4.9 - - - +
54B ASP* 2.8 50.8 + - + +
142B GLU* 4.0 17.0 - - - +
143B SER* 1.3 75.6 + - - +
145B LEU* 1.3 69.4 + - - +
146B SER* 4.1 7.3 + - - +
151B ARG* 3.6 39.0 - - + +
153B GLY 3.5 6.3 - - - +
154B CYS* 3.7 21.8 - - - -
2485B LPE 3.6 2.0 - - - -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA* 4.6 3.6 - - + -
47B LEU* 3.9 32.5 - - + -
51B LEU* 3.4 33.0 - - + -
52B LYS 3.4 11.4 - - - +
53B VAL* 3.9 15.3 - - + +
144B VAL* 1.3 71.7 - - - +
146B SER* 1.3 63.1 + - - +
151B ARG* 3.7 2.8 - - - +
152B LEU* 2.7 31.7 + - + -
153B GLY 2.8 21.5 + - - +
2485B LPE 3.1 42.5 + - - +
3322B ACT 4.0 8.1 - - + -
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.6 4.9 - - - +
52B LYS* 2.7 61.8 + - - +
54B ASP* 4.7 2.4 + - - -
144B VAL* 4.8 7.8 + - - +
145B LEU* 1.3 77.6 - - - +
147B SER* 1.3 62.8 + - - +
149B GLY* 4.8 7.6 + - - -
150B LYS 3.2 23.1 - - - -
151B ARG* 4.0 4.0 - - - -
152B LEU* 3.9 6.1 - - - +
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B SER 3.9 8.9 + - - -
49B SER 4.7 0.2 + - - -
50B PRO* 2.7 31.4 + - - +
51B LEU* 4.7 0.9 - - - -
52B LYS* 5.6 0.4 - - - -
146B SER* 1.3 76.3 - - - +
148B SER* 1.3 71.8 + - - +
149B GLY 3.1 0.2 - - - -
150B LYS* 3.0 24.9 + - - +
152B LEU* 3.6 21.1 - - - +
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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