Contacts of the strand formed by residues 137 - 147 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C MET 6.0 0.9 - - - -
59C LYS* 4.4 6.1 - - - -
60C GLU 5.7 0.9 - - - -
135C THR 3.2 2.7 + - - -
136C THR* 1.3 79.8 - - - +
138C ASN* 1.3 67.1 + - - -
139C TYR* 3.6 9.3 - - - -
160C SER* 3.3 3.3 - - - -
161C LEU 2.9 34.0 + - - +
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Residues in contact with ASN 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C MET* 3.5 26.7 + - - +
3C SER* 3.1 25.9 + - - +
59C LYS* 3.6 5.1 - - - +
60C GLU* 2.9 64.7 + - + +
65C TRP* 4.1 8.5 - - + -
137C GLY* 1.3 75.9 - - - -
139C TYR* 1.3 62.0 + - - +
159C ALA 3.8 4.3 - - - +
160C SER* 2.6 28.0 + - - +
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Residues in contact with TYR 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LEU* 4.5 2.0 - - + -
58C GLU 3.3 16.6 - - - +
59C LYS* 3.5 29.6 - - + +
65C TRP* 3.8 5.8 - - - -
68C ILE* 3.8 13.7 - - + -
134C LEU 3.5 10.2 + - - -
135C THR* 2.6 37.1 + - - -
137C GLY 3.6 18.4 - - - -
138C ASN* 1.3 76.5 - - - +
140C ARG* 1.3 64.6 + - - +
158C ALA* 3.4 4.9 - - - +
159C ALA 2.8 32.2 + - - +
161C LEU* 3.8 21.5 - - + -
2486C PFS 3.4 56.5 - - + +
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Residues in contact with ARG 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C VAL 3.8 0.5 - - - +
57C LEU* 3.6 2.3 - - - +
58C GLU* 2.6 71.0 + - + +
65C TRP* 3.4 60.3 - - + +
139C TYR* 1.3 78.3 - - - +
141C ILE* 1.3 64.1 + - - +
157C ILE 3.2 11.0 - - - +
158C ALA* 4.5 7.2 - - + -
2486C PFS 3.4 2.9 - - - -
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Residues in contact with ILE 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU* 4.2 30.3 - - + -
56C VAL 3.2 17.7 - - - +
57C LEU* 4.0 15.0 - - + -
75C GLY 5.5 1.1 - - - +
140C ARG* 1.3 78.3 - - - +
142C GLU* 1.3 69.9 + - - +
143C SER* 5.5 3.4 - - - +
155C ILE* 3.9 1.2 - - + +
156C LYS* 3.3 4.7 - - - +
157C ILE* 2.8 48.3 + - + +
2486C PFS 3.2 36.6 - - + +
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Residues in contact with GLU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C CYS* 4.2 0.5 - - - +
54C ASP 3.5 1.9 - - - +
55C LEU* 3.4 4.2 - - - -
56C VAL* 2.9 54.1 + - + +
141C ILE* 1.3 76.1 - - - +
143C SER* 1.3 62.0 + - - +
144C VAL* 4.4 12.1 - - + +
154C CYS* 4.1 20.5 - - - -
155C ILE 3.4 9.0 - - - +
156C LYS* 2.9 36.7 + - + -
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Residues in contact with SER 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C VAL* 4.0 3.3 - - - +
54C ASP 3.4 3.6 - - - -
55C LEU* 3.2 24.9 - - - +
141C ILE* 4.2 5.1 - - - +
142C GLU* 1.3 72.8 - - - +
144C VAL* 1.3 64.0 + - - +
154C CYS* 3.3 1.9 - - - -
155C ILE* 2.9 38.9 + - - +
2488C LPE 2.9 46.3 + - - -
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LYS 3.4 1.6 - - - +
53C VAL* 3.4 5.6 - - - +
54C ASP* 2.9 54.5 + - + +
142C GLU* 4.4 15.5 - - + +
143C SER* 1.3 78.1 + - - +
145C LEU* 1.3 70.9 + - - +
146C SER* 4.7 5.4 - - - -
151C ARG* 4.1 18.2 - - + +
153C GLY 3.5 9.6 - - - +
154C CYS* 3.8 21.1 - - - -
2488C LPE 4.9 0.2 - - - -
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Residues in contact with LEU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ALA* 4.7 2.7 - - + -
47C LEU* 3.9 31.2 - - + -
51C LEU* 3.8 28.5 - - + -
52C LYS 3.3 13.2 - - - +
53C VAL* 3.7 19.5 - - + -
143C SER 4.2 0.6 + - - -
144C VAL* 1.3 73.0 - - - +
146C SER* 1.3 62.8 + - - +
151C ARG* 4.0 1.4 - - - -
152C LEU* 2.8 29.9 + - + -
153C GLY 2.8 18.2 + - - +
2488C LPE 3.9 38.3 + - - +
3324C ACT 4.3 10.5 - - + +
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Residues in contact with SER 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.6 4.9 - - - +
52C LYS* 2.8 63.1 + - - +
54C ASP* 4.4 4.5 + - - -
144C VAL* 4.7 7.4 - - - -
145C LEU* 1.3 76.4 - - - +
147C SER* 1.3 63.7 + - - +
149C GLY* 5.0 6.8 + - - -
150C LYS 3.4 21.3 - - - -
151C ARG* 4.1 4.0 - - - -
152C LEU* 3.9 6.1 - - - -
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Residues in contact with SER 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C SER 3.6 10.2 + - - -
49C SER 4.8 0.3 + - - -
50C PRO* 2.7 28.8 + - - +
51C LEU* 4.6 0.4 - - - -
52C LYS* 5.7 0.7 - - - -
146C SER* 1.3 76.6 - - - +
148C SER* 1.3 72.6 + - - +
149C GLY 3.2 1.1 - - - -
150C LYS* 2.9 24.4 + - - +
152C LEU* 3.7 22.0 - - - +
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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