Contacts of the strand formed by residues 137 - 145 (chain H) in PDB entry 4XLN
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 LYS 137 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59H GLU 5.7 0.2 - - - +
60H ASP* 5.0 10.0 - - - +
68H ILE* 4.2 15.6 - - - +
69H PRO 4.7 7.5 + - - +
70H GLY* 5.1 0.4 - - - -
71H VAL* 4.6 2.9 - - - +
103H ALA 4.0 1.6 - - - -
104H GLU* 5.2 2.0 - - + +
132H LEU* 4.0 1.7 - - - +
135H GLY* 3.3 20.4 + - - +
136H GLY* 1.3 72.4 - - - +
138H LEU* 1.3 65.0 + - - +
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Residues in contact with LEU 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H ILE* 3.9 24.2 - - + -
59H GLU* 5.1 4.7 - - - +
68H ILE* 4.8 17.9 - - + -
71H VAL* 4.6 7.0 - - + -
101H LEU* 3.7 28.3 - - + -
102H ARG* 3.6 5.1 + - - +
103H ALA* 2.9 42.1 + - + +
109H VAL* 6.0 0.2 - - + -
130H ALA* 5.6 7.6 - - + -
132H LEU* 4.1 19.1 - - + -
137H LYS* 1.3 77.3 - - - +
139H TYR* 1.3 69.6 + - - +
140H MET* 3.8 25.1 - - + -
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Residues in contact with TYR 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H TYR* 4.9 1.7 - + - -
58H ILE* 3.6 1.7 - - - +
59H GLU* 2.8 64.6 + - + +
100H ILE* 3.4 31.9 - - + +
101H LEU 3.2 18.4 - - - -
102H ARG* 3.4 42.4 - - + +
138H LEU* 1.3 79.5 - - - +
140H MET* 1.3 70.0 + - - +
141H GLU* 3.2 40.1 + - + +
161H ARG* 4.3 9.2 - - - -
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Residues in contact with MET 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H VAL* 4.4 4.5 - - + -
57H TYR* 3.1 15.9 - - - +
58H ILE* 3.8 20.4 - - + -
78H ILE* 3.8 27.8 - - + -
82H LEU* 4.3 19.1 - - + -
99H LEU 4.0 0.2 - - - +
100H ILE* 3.7 2.1 - - - -
101H LEU* 2.9 58.0 + - + +
114H PHE* 4.7 3.2 - - - -
129H ILE* 5.2 5.8 - - + -
138H LEU* 3.8 16.8 - - + -
139H TYR* 1.3 78.7 - - - +
141H GLU* 1.3 64.1 + - - +
142H VAL* 4.2 19.1 - - + -
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Residues in contact with GLU 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H VAL* 3.6 1.0 - - - -
57H TYR* 2.9 49.9 + - + +
98H THR* 4.5 10.6 - - + +
99H LEU 3.3 5.2 - - - +
100H ILE* 3.7 15.4 - - + +
139H TYR* 3.2 31.7 + - + +
140H MET* 1.3 76.7 - - - +
142H VAL* 1.3 63.1 + - - +
143H ARG 4.2 0.3 + - - -
161H ARG* 2.6 36.2 + - - +
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Residues in contact with VAL 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H VAL* 4.0 17.9 - - + -
55H SER 3.7 4.0 - - - +
56H VAL* 3.7 25.6 - - + -
82H LEU* 4.4 7.0 - - + -
85H LEU* 5.5 2.7 - - + -
98H THR* 3.2 7.3 - - - +
99H LEU* 2.9 62.8 + - + -
114H PHE* 3.6 28.7 - - + -
140H MET* 4.3 10.5 - - - -
141H GLU* 1.3 77.5 - - - +
143H ARG* 1.3 59.9 + - - +
144H VAL* 4.1 3.8 + - + -
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Residues in contact with ARG 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H VAL* 3.1 3.9 - - - +
54H THR* 2.5 45.2 + - + +
55H SER* 3.0 18.2 + - - +
96H SER* 4.7 9.5 + - - -
97H THR 3.6 9.6 - - - +
98H THR* 4.5 12.7 + - + +
141H GLU 4.2 0.4 + - - -
142H VAL* 1.3 72.8 - - - +
144H VAL* 1.3 56.5 + - - +
145H ASP* 3.1 28.2 + - - +
158H ILE* 4.2 17.1 - - - +
160H ASP* 2.8 42.6 + - - +
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Residues in contact with VAL 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H THR* 4.8 1.3 - - - +
52H ALA 4.3 3.1 - - - +
53H VAL* 3.6 33.9 - - + +
85H LEU* 6.1 1.6 - - + -
87H VAL* 3.7 27.1 - - + -
89H PHE* 3.6 21.7 - - + -
96H SER* 3.2 3.1 - - - -
97H THR* 2.9 48.4 + - + -
99H LEU* 3.6 25.1 - - + -
142H VAL* 4.5 3.6 - - + -
143H ARG* 1.3 71.9 - - - +
145H ASP* 1.3 70.4 + - - +
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Residues in contact with ASP 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H GLY 3.6 1.3 - - - +
51H THR 3.3 20.4 - - - +
52H ALA 3.4 12.3 + - - +
54H THR* 3.2 19.2 - - + +
89H PHE* 4.4 3.6 - - - -
95H ALA 3.4 5.5 - - - +
96H SER* 3.3 21.3 - - - -
143H ARG* 3.1 31.0 + - - +
144H VAL* 1.3 78.7 - - - +
146H ARG* 1.3 62.3 + - - +
147H GLY 3.8 0.2 - - - -
171H PHE* 3.7 9.2 - - + -
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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