Contacts of the strand formed by residues 93 - 101 (chain I) 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 PRO 93 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I GLY* 3.0 28.6 + - - -
75I ASP 3.6 15.3 - - - +
77I PRO* 3.7 13.7 - - + -
92I ALA* 1.3 86.7 - - + +
94I LEU* 1.3 60.4 + - - +
95I TYR* 3.5 25.9 + - + +
114I PHE* 3.4 19.7 - - + -
116I GLY 3.4 7.6 - - - +
117I HIS* 3.8 18.6 - - + +
298L GLY 4.1 4.7 - - - +
299L ARG* 5.8 0.9 - - + -
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Residues in contact with LEU 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I ILE* 4.9 2.9 - - + -
48I PHE* 4.4 9.2 - - + -
71I TYR* 3.7 26.9 - - + -
72I ARG 3.2 17.3 - - - +
73I ILE* 4.5 8.7 - - + -
92I ALA 3.5 3.3 + - - +
93I PRO* 1.3 70.8 - - - +
95I TYR* 1.3 60.5 + - - +
114I PHE* 3.7 2.4 - - - -
115I LEU* 3.1 46.9 + - + +
116I GLY 2.6 18.0 + - - +
118I LEU* 4.9 22.4 - - + -
344I PHE* 3.7 33.9 - - + -
378I LEU* 5.4 0.7 - - + -
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Residues in contact with TYR 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71I TYR* 3.4 1.4 - - - -
72I ARG* 2.5 90.7 + - + +
74I GLY* 4.4 3.8 - - - -
93I PRO* 3.5 37.1 - - + +
94I LEU* 1.3 71.2 - - - +
96I ALA* 1.3 60.6 + - - +
97I ARG* 3.9 0.7 + - - +
112I GLU* 3.5 27.7 - - - +
113I VAL 3.7 4.9 - - - +
114I PHE* 3.6 24.2 - + + -
297L LEU 4.9 3.4 + - - -
298L GLY* 4.0 17.6 + - - -
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Residues in contact with ALA 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I PHE* 4.6 10.5 - - + -
68I PHE* 5.9 1.1 - - + -
70I GLU 3.9 5.4 - - - +
71I TYR* 4.3 3.1 - - + +
94I LEU 3.5 3.4 + - - -
95I TYR* 1.3 72.9 - - - +
97I ARG* 1.3 61.0 + - - +
98I LEU* 4.0 2.9 - - + -
112I GLU* 3.5 1.6 - - - +
113I VAL* 2.9 45.7 + - + +
115I LEU* 3.6 35.8 - - + +
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Residues in contact with ARG 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I PHE* 4.1 3.5 - - - -
69I LEU* 2.9 42.9 + - + +
70I GLU* 2.6 47.2 + - + +
71I TYR* 5.2 0.4 - - - -
72I ARG 6.0 0.2 - - - +
95I TYR 3.9 1.3 + - - +
96I ALA* 1.3 71.4 - - - +
98I LEU* 1.3 62.5 + - - +
110I GLU* 2.8 44.1 + - - +
112I GLU* 3.6 36.8 - - + +
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Residues in contact with LEU 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I PHE* 3.9 18.8 - - + -
66I LEU* 3.6 38.6 - - + -
67I ASP 3.2 14.6 - - - +
68I PHE* 4.6 1.1 - - + -
69I LEU* 3.6 12.4 - - - +
96I ALA* 5.2 3.1 - - + -
97I ARG* 1.3 75.5 - - - +
99I GLN* 1.3 64.1 + - - +
110I GLU* 3.7 9.7 - - - +
111I ASP 3.7 16.3 + - - +
113I VAL* 3.6 39.3 - - + +
369I PRO* 3.7 6.7 - - + -
373I VAL* 3.6 17.0 - - + -
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Residues in contact with GLN 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I LEU* 3.3 8.7 - - - +
67I ASP* 2.9 59.4 + - + +
69I LEU* 3.6 18.2 - - + +
98I LEU* 1.3 77.1 - - - +
100I LEU* 1.3 60.6 + - - +
101I ILE* 3.5 31.0 + - + +
108I ILE* 5.4 2.1 - - - +
109I LYS 4.2 2.9 - - - -
110I GLU* 3.1 34.9 - - + +
369I PRO* 4.9 0.9 - - - -
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Residues in contact with LEU 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I LEU* 3.6 31.4 - - + -
65I VAL 4.3 0.4 - - - -
66I LEU* 3.8 10.7 - - + +
99I GLN* 1.3 69.9 - - - +
101I ILE* 1.3 61.0 + - - +
102I HIS* 3.4 26.9 - - + +
107I LEU* 3.7 1.6 - - + +
109I LYS* 3.0 55.8 + - + +
367I LEU* 3.1 32.8 - - + +
368I THR 4.5 0.4 - - - +
369I PRO* 3.7 15.9 - - + +
372I LEU* 3.8 17.7 - - + -
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Residues in contact with ILE 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I LEU* 3.3 3.7 - - - +
65I VAL* 2.9 59.8 + - + +
67I ASP* 4.8 4.0 - - + -
99I GLN* 3.5 45.8 - - + +
100I LEU* 1.3 83.4 - - - +
102I HIS* 1.3 66.0 + - - +
103I LYS* 5.6 0.7 - - - -
107I LEU 3.8 1.3 - - - -
108I ILE* 3.6 39.9 - - + -
109I LYS 4.8 0.2 - - - +
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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