Contacts of the strand formed by residues 50 - 62 (chain A) in PDB entry 4XWX
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 VAL 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A HIS* 3.7 39.0 - - + +
44A LYS* 3.9 22.9 - - + +
45A VAL* 3.8 21.8 - - + -
49A GLY* 1.3 76.5 - - - -
51A SER* 1.3 66.8 + - - +
52A TYR* 3.5 32.1 - - + +
124A LEU 3.6 1.2 - - - +
125A THR* 3.3 1.5 - - - -
126A VAL 2.8 35.9 + - - +
193A THR* 4.1 7.0 - - + -
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 5.3 2.6 - - - +
49A GLY 4.2 1.5 + - - -
50A VAL* 1.3 75.2 - - - +
52A TYR* 1.3 71.9 + - - +
53A LEU* 6.1 0.9 - - - -
123A THR* 3.9 14.9 - - - +
124A LEU 3.1 5.6 - - - -
125A THR* 3.0 23.6 + - - +
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Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 4.6 0.9 - + - -
50A VAL* 3.5 27.8 - - + +
51A SER* 1.3 78.2 - - - +
53A LEU* 1.3 65.1 + - - +
54A VAL* 3.7 18.0 + - + -
123A THR* 3.4 2.8 - - - -
124A LEU* 2.8 49.9 + - + +
126A VAL* 3.7 21.5 - - + -
186A LEU* 4.3 21.3 - - + -
189A ASP* 2.6 41.2 + - + -
190A VAL* 3.7 28.0 - - + -
193A THR* 2.9 21.3 + - - -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A SER* 6.0 1.1 - - - -
52A TYR* 1.3 74.3 - - - +
54A VAL* 1.3 61.8 + - - +
122A ILE 3.5 6.5 - - - +
123A THR* 3.7 26.9 - - + +
183A PRO* 3.2 29.4 - - + +
186A LEU* 4.4 5.0 - - + +
305A EDO 4.5 2.0 + - - -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 4.0 17.3 - - + -
53A LEU* 1.3 81.6 - - - +
55A ARG* 1.3 60.4 + - - +
121A PRO* 3.5 5.0 - - - +
122A ILE* 2.9 52.9 + - + +
124A LEU* 4.0 15.3 - - + -
180A LEU* 4.3 16.6 - - + -
181A GLU 3.6 11.7 - - - +
182A CYS* 3.8 24.2 - - - -
183A PRO* 4.2 4.5 - - + -
186A LEU* 5.3 1.1 - - + -
190A VAL* 4.8 5.6 - - + -
305A EDO 4.1 8.4 + - - -
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 1.3 75.0 - - - +
56A TYR* 1.3 64.7 + - - +
57A MET* 3.6 19.7 + - - +
89A VAL* 4.0 3.7 - - - +
90A PRO* 3.5 26.8 + - - +
91A GLY* 3.8 19.2 + - - -
92A ALA 4.0 2.0 - - - +
119A GLY* 2.9 47.1 + - - +
120A MET 3.6 5.8 - - - +
121A PRO* 4.3 4.5 - - + +
180A LEU* 3.5 3.0 - - - -
181A GLU* 2.9 55.4 + - + +
305A EDO 3.8 14.1 - - - +
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Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL 4.1 1.0 - - - -
55A ARG* 1.3 72.4 - - - +
57A MET* 1.3 55.5 + - - +
58A GLY* 3.6 38.4 - - - -
59A CYS* 3.8 4.9 + - - +
114A ASN* 5.6 0.6 + - - -
117A PHE* 3.4 42.6 - + + +
119A GLY* 2.7 31.2 + - - -
120A MET 3.0 17.8 + - - +
122A ILE* 4.1 20.7 - - + +
133A LEU* 3.6 29.2 - - + -
142A ILE* 4.2 10.5 - - + -
145A HIS* 5.8 0.2 - + - -
173A ASN* 5.0 1.7 + - - -
178A HIS* 2.8 38.7 + - + -
179A ILE 3.8 8.7 - - - -
180A LEU* 3.9 9.6 - - + -
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Residues in contact with MET 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.6 41.5 - - - +
56A TYR* 1.3 79.6 - - - +
58A GLY* 1.3 60.1 + - - +
85A VAL* 3.3 36.6 - - + +
86A CYS* 5.0 2.9 - - - -
89A VAL* 3.9 15.6 - - + +
92A ALA* 3.5 34.3 - - + -
115A LEU* 4.2 0.9 - - - +
118A ALA* 3.5 15.1 - - - +
119A GLY 4.1 7.0 - - - +
163A TYR* 4.3 9.9 - - + +
179A ILE* 2.8 18.7 + - + +
181A GLU* 3.5 27.8 - - + +
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Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TYR* 3.6 29.4 + - - -
57A MET* 1.3 79.7 - - - +
59A CYS* 1.3 62.1 + - - +
85A VAL* 4.6 2.9 - - - -
114A ASN 3.5 13.9 - - - -
115A LEU* 4.9 0.9 - - - -
118A ALA* 3.8 8.8 - - - +
179A ILE* 3.1 25.6 + - - +
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Residues in contact with CYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TYR* 4.0 2.9 - - - -
58A GLY* 1.3 72.8 - - - -
60A VAL* 1.3 65.0 + - - +
61A GLU 4.3 0.2 - - - -
85A VAL* 4.6 3.0 - - - +
113A SER* 3.3 5.2 - - - -
114A ASN* 2.8 47.8 + - - +
173A ASN* 3.4 35.7 - - - -
176A ALA* 3.9 9.0 - - + -
177A CYS 3.1 15.7 - - - +
178A HIS* 3.4 26.9 - - + +
302A EDO 4.4 2.0 - - - -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A CYS* 1.3 79.8 - - - +
61A GLU* 1.3 70.3 + - - +
62A VAL* 3.7 2.6 - - - +
81A ALA* 4.0 22.2 - - + +
84A LEU* 4.2 13.2 - - + -
85A VAL* 3.9 21.5 - - + -
110A LEU* 3.6 31.0 - - + -
111A GLY 3.7 18.8 - - - +
112A ARG 3.4 5.6 - - - +
113A SER* 4.0 9.9 - - - +
176A ALA* 4.1 2.0 - - - -
177A CYS 2.8 33.4 + - - +
179A ILE* 5.4 0.2 - - + -
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 1.3 75.3 - - - +
62A VAL* 1.3 61.4 + - - +
63A LEU* 3.7 24.4 - - + +
110A LEU* 3.5 5.9 - - - +
111A GLY* 2.8 28.0 + - - -
112A ARG* 2.8 43.2 + - - +
173A ASN 4.9 0.2 - - - +
174A GLN* 5.2 9.0 - - + +
175A ARG 3.7 9.9 - - - +
176A ALA* 4.2 0.2 - - - +
302A EDO 3.3 30.3 + - - +
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL 3.7 1.8 - - - +
61A GLU* 1.3 77.7 - - - +
63A LEU* 1.3 63.5 + - - +
64A GLN 3.3 23.3 - - - +
66A MET* 4.4 13.7 - - - -
77A VAL* 4.7 3.6 - - + -
109A ILE* 3.4 14.8 - - + +
110A LEU* 4.0 11.0 - - + -
167A VAL* 4.5 8.7 - - + -
175A ARG* 2.9 48.1 + - + +
176A ALA 4.1 1.1 - - - -
177A CYS* 3.7 34.5 - - + +
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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